Production of Renewable Hydrocarbon Compositions

ABSTRACT

Provided herein are processes and microorganisms which utilize both protein hydrolysates and carbohydrates from biomass feedstocks to produce renewable hydrocarbon compositions. Advantages of the disclosed methods may be recognized in fuel blends comprising such hydrocarbon compositions.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional application of U.S. patent application Ser. No. 14/428,197, filed on Mar. 13, 2015 which is a 371 of International Application No. PCT/US2013/060871, filed on Sep. 20, 2013 which is related to and claims the benefit of priority of U.S. Provisional Application Ser. No. 61/704,295, filed on Sep. 21, 2012, the entirety of each is herein incorporated herein by reference.

REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY

The content of the electronically submitted sequence listing in ASCII text file (Name: CL5716USDIV_SeqList_ST25.txt) filed with the application is incorporated herein by reference in its entirety.

FIELD OF THE INVENTION

The invention relates to methods for fermentative co-production of butanol and fusel alcohols, as well as recombinant host cells thereof.

BACKGROUND OF THE INVENTION

Butanol is an important industrial chemical, useful as a fuel, fuel component and fuel additive, as a chemical solvent, feedstock in various chemical markets, such as the plastics industry, and as a food grade extractant in the food and flavor industry. Each year 10 to 12 billion pounds of butanol are produced by petrochemical means and the need for this commodity chemical will likely increase in the future.

Methods for the chemical synthesis of isobutanol are known, such as oxo synthesis, catalytic hydrogenation of carbon monoxide (Ullmann's Encyclopedia of Industrial Chemistry, 6th edition, 2003, Wiley-VCH Verlag GmbH and Co., Weinheim, Germany, Vol. 5, pp. 716-719) and Guerbet condensation of methanol with n-propanol (Carlini, et al., J. Molec. Catal. A. Chem. 220:215-220, 2004). These processes use starting materials derived from petrochemicals. The production of isobutanol from plant-derived raw materials would represent an advance in the art.

Isobutanol is produced biologically as a by-product of yeast fermentation. It is a component of “fusel oil” that forms as a result of the incomplete metabolism of amino acids by fungi. Isobutanol is specifically produced from catabolism of L-valine. After the amine group of L-valine is harvested as a nitrogen source, the resulting α-keto acid is decarboxylated and reduced to isobutanol by enzymes of the so-called Ehrlich pathway (Dickinson, et al., J. Biol. Chem. 273:25752-25756, 1998). U.S. Pat. Nos. 7,851,188 and 7,993,889 describe enzymatic pathways for the production of isobutanol in recombinant microorganisms.

An increase in the yield of C3-C5 alcohols from carbohydrates was shown when amino acids leucine, isoleucine, and/or valine were added to the growth medium as the nitrogen source (International Publication No. WO 2005/040392). Similarly, Lilly, et al. (FEMS Yeast Res. 6(5):726-743, 2006) have demonstrated that the addition of a high concentration of valine to a fermentation medium increased Saccharomyces cerevisiae production of isobutanol, isobutyric acid, propanol and propionic acid concentrations.

Nako, et al (International Publication No. WO 2007/032522) note that amyl alcohol and/or isobutanol and/or isoamyl acetate levels in yeast used for the production of alcoholic beverages may be altered via manipulation of the BAT1 and BAT2 genes. See also, Chen, et al. (Biotechnology for Biofuels 4:21, 2011) and Yoshimoto, et al. (Appl. Microbiol. Biotechnol. 59:501-508, 2002).

U.S. Patent Application Publication No. 2010/0209986 describes means to produce metabolically-modified microorganisms useful for producing biofuels (e.g., isobutanol, 1-butanol, 1-propanol, 2-methyl-1-butanol, 3-methyl-1-butanol and 2-phenylethanol) from a suitable substrate. The methodology utilizes the organism's native metabolites in the amino acid biosynthetic pathway to produce biofuels by increasing flux towards the production of a 2-keto acid. The microorganism may comprise a 2-keto-acid decarboxylase, preferably selected from the group consisting of Pdc, Pdc1, Pdc5, Pdc6, Aro10, Thi3, KivD, and KdcA.

U.S. Patent Application Publication No. 2012/0045809 describes a recombinant eukaryotic microorganism capable of producing isobutanol from a carbon source, said recombinant eukaryotic microorganism comprising an isobutanol producing metabolic pathway, wherein said recombinant eukaryotic microorganism may overexpress a valine transaminase (encoded, e.g., by BAT1 or BAT2).

Enzymatic saccharification of cellulosic and/or lignocellulosic biomass may be employed to break down cellulose and hemicellulose to produce a hydrolysate containing sugars suitable for consumption by microorganisms (Lynd, et al., Microbiol. Mol. Biol. Rev. 66:506-577, 2002). U.S. Pat. No. 5,231,017 describes a process for producing ethanol from raw materials, wherein a protease is utilized in combination with alpha-amylase and glucoamylase, to increase the rate and yield of ethanol production. Huo, et al. (Nature Biotechnol. 29(4):346-352, 2011) suggest that a nitrogen-centric metabolic engineering strategy could be utilized to utilize proteins as feedstock for the production of biofuels.

Improvements and alternatives for the biosynthesis of butanol directly from plant-derived raw materials would improve economic viability and would represent an advance in the art.

SUMMARY OF THE INVENTION

Provided herein are methods for producing a renewable hydrocarbon composition comprising isobutanol, the methods comprising: a) providing a biomass feedstock; b) processing the biomass feedstock to produce a processed feedstock slurry comprising protein hydrolysates and fermentable carbohydrate; c) adding the processed feedstock slurry to a fermentation medium; d) contacting the fermentation medium comprising processed feedstock slurry with a recombinant yeast host cell modified to produce a fermentation composition comprising isobutanol from carbohydrate and from protein hydrolysate; and (e) recovering a renewable hydrocarbon composition from the fermentation composition by distillation; whereby the renewable hydrocarbon composition comprising at least about 90% isobutanol is produced. In embodiments, processing the biomass feedstock to produce a processed feedstock slurry comprising protein hydrolysates and oligosaccharides comprises liquefying the biomass feedstock in the presence of at least one protease. In embodiments, processing the biomass feedstock to produce a processed feedstock slurry comprising protein hydrolysates and oligosaccharides comprises: liquefying the biomass feedstock to create a feedstock slurry comprising oligosaccharides, undissolved solids, and water; separating at least a portion of the undissolved solids from the feedstock slurry of step (a) to generate: 1) an aqueous solution comprising oligosaccharides; and 2) a wet cake co-product comprising solids; hydrolyzing the wet cake co-product to produce protein hydrolysates; and, mixing the aqueous solution comprising oligosaccharides with the protein hydrolysates to produce a processed feedstock slurry comprising protein hydrolysates and oligosaccharides. In embodiments, the wet cake co-product is hydrolyzed by a means selected from the group consisting of: acid hydrolysis, base hydrolysis and enzymatic hydrolysis. In embodiments, the recombinant yeast host cell modified to produce isobutanol from carbohydrate and from protein hydrolysate comprises: a heterologous isobutanol biosynthetic pathway for production of isobutanol; and, at least one upregulated Ehrlich pathway gene for production of fusel oil. In embodiments, the recovered renewable hydrocarbon composition comprises at least about 90% isobutanol and further comprises greater than about 0.3% isoamyl alcohol. In embodiments, the recombinant yeast host cell modified to produce isobutanol from carbohydrate and from protein hydrolysate further comprises: at least one downregulated Ehrlich pathway gene for production of fusel oil. In embodiments, the recovered renewable hydrocarbon composition comprises less than about 0.3% isoamyl alcohol. In embodiments, the renewable hydrocarbon composition comprises higher total carbon content than a composition consisting essentially of isobutanol.

In embodiments, the methods provided herein further comprise blending an amount of the renewable hydrocarbon composition with gasoline whereby a fuel blend is produced. In embodiments, the fuel blend comprises at least one of increased volumetric energy density or decreased vapor pressure as compared to a blend comprising an equivalent amount of a composition consisting essentially of isobutanol. In embodiments, the fuel blend further comprises ethanol. In embodiments, the fuel blend comprising ethanol comprises decreased phase separation when contacted by water as compared to a fuel blend comprising ethanol and an equivalent amount of a composition consisting essentially of isobutanol.

Also provided herein are methods of producing a butanol and fusel oil mixture from a biomass feedstock comprising: providing a biomass feedstock; processing the biomass feedstock to produce a processed feedstock slurry comprising protein hydrolysates and oligosaccharides; saccharifying the oligosaccharides of the processed feedstock slurry to produce a fermentation composition comprising fermentable sugars and protein hydrolysates; fermenting a recombinant yeast in the presence of the fermentation composition, said recombinant yeast comprising: a heterologous butanol biosynthetic pathway for production of butanol; and, at least one upregulated Ehrlich pathway gene for production of fusel oil; whereby a butanol and fusel oil mixture is produced; and, recovering the butanol and fusel oil mixture; wherein the yield of the butanol and fusel oil mixture per unit weight of biomass feedstock is improved. In embodiments, processing the biomass feedstock to produce a processed feedstock slurry comprising protein hydrolysates and oligosaccharides comprises liquefying the biomass feedstock in the presence of at least one protease. In embodiments, processing the biomass feedstock to produce a processed feedstock slurry comprising protein hydrolysates and oligosaccharides comprises: liquefying the biomass feedstock to create a feedstock slurry comprising oligosaccharides, undissolved solids, and water; separating at least a portion of the undissolved solids from the feedstock slurry step to generate: an aqueous solution comprising oligosaccharides and a wet cake co-product comprising solids; hydrolyzing the wet cake co-product of step (2)(ii) to produce protein hydrolysates; and mixing the aqueous solution comprising oligosaccharides with the protein hydrolysates to produce a processed feedstock slurry comprising protein hydrolysates and oligosaccharides.

In embodiments, the undissolved solids are separated from the feedstock slurry by decanter bowl centrifugation, tricanter centrifugation, disk stack centrifugation, filtering centrifugation, decanter centrifugation, filtration, vacuum filtration, beltfilter, pressure filtration, screen filtration, microfiltration, screen separation, grating, porous grating, flotation, hydroclone, filter press, screwpress, gravity settler, vortex separator, or combinations thereof. In embodiments, the wet cake co-product is hydrolyzed by a means selected from the group consisting of: acid hydrolysis, base hydrolysis and enzymatic hydrolysis.

In embodiments provided herein, the feedstock in the fermentation process comprises one or more fermentable sugars derived from corn grain, corn cobs, crop residues such as corn husks, corn stover, grasses, wheat, rye, wheat straw, barley, barley straw, hay, rice straw, switchgrass, waste paper, sugar cane bagasse, sorghum, sugar cane, soy, components obtained from milling of grains, cellulosic material, lignocellulosic material, trees, branches, roots, leaves, wood chips, sawdust, shrubs and bushes, vegetables, fruits, flowers, animal manure, and mixtures thereof. In embodiments provided herein, the recombinant yeast is Saccharomyces, Schizosaccharomyces, Hansenula, Candida, Kluyveromyces, Yarrowia, Issatchenkia, or Pichia. In embodiments, the recombinant yeast is Saccharomyces cerevisiae.

In embodiments of the methods provided herein, the at least one upregulated Ehrlich pathway gene is selected from the group consisting of: a gene encoding a polypeptide having aromatic aminotransferase activity, said polypeptide having at least about 90% identity to ARO8 (SEQ ID NO:2) or ARO9 (SEQ ID NO:4); a gene encoding a polypeptide having branched chain amino acid transferase activity, said polypeptide having at least about 90% identity to BAT1 (SEQ ID NO:8) or BAT2 (SEQ ID NO:10); a gene encoding a polypeptide having phenylpyruvate decarboxylase activity, said polypeptide having at least about 90% identity to ARO10 (SEQ ID NO:6); a gene encoding a polypeptide having Pyruvate decarboxylase activity, said polypeptide having at least about 90% identity to PDC1 (SEQ ID NO:12), PDC5 (SEQ ID NO:14) or PDC6 (SEQ ID NO:16); a gene encoding a polypeptide having Alpha-ketoisocaproate decarboxylase activity, said polypeptide having at least about 90% identity to THI3 (SEQ ID NO:18); a gene encoding a polypeptide having Alcohol dehydrogenase activity, said polypeptide having at least about 90% identity to ADH1 (SEQ ID NO:20), ADH2 (SEQ ID NO:22), ADH3 (SEQ ID NO:24), ADH4 (SEQ ID NO:26), ADH5 (SEQ ID NO:28), ADH6 (SEQ ID NO:30) or SFA1 (SEQ ID NO:32); a gene encoding a polypeptide having aryl-alcohol dehydrogenase activity, said polypeptide having at least about 90% identity to AAD3 (SEQ ID NO:34), AAD4 (SEQ ID NO:36), AAD6 (SEQ ID NO:30), AAD10 (SEQ ID NO:40), AAD14 (SEQ ID NO:42), AAD15 (SEQ ID NO:44), AAD16 (SEQ ID NO:46) or YPL088W (SEQ ID NO:48); a gene encoding a polypeptide having Aldehyde dehydrogenase activity, said polypeptide having at least about 90% identity to ALD2 (SEQ ID NO:52), ALD3 (SEQ ID NO:54), ALD4 (SEQ ID NO:56), ALD5 (SEQ ID NO:58) or ALD6 (SEQ ID NO:60); and, a gene encoding a polypeptide having ATP-binding ATP transporter activity, said polypeptide having at least about 90% identity to PDR12 (SEQ ID NO:50).

In embodiments of the methods provided herein, the butanol biosynthetic pathway is selected from the group consisting of: an isobutanol biosynthetic pathway comprising the following substrate to product conversions: pyruvate to acetolactate, acetolactate to 2,3-dihydroxyisovalerate, 2,3-dihydroxyisovalerate to α-ketoisovalerate, α-ketoisovalerate to isobutyraldehyde, and isobutyraldehyde to isobutanol; an isobutanol biosynthetic pathway comprising the following substrate to product conversions: pyruvate to acetolactate, acetolactate to 2,3-dihydroxyisovalerate, 2,3-dihydroxyisovalerate to α-ketoisovalerate, α-ketoisovalerate to isobutyryl-CoA, isobutyryl-CoA to isobutyraldehyde, and isobutyraldehyde to isobutanol; an isobutanol biosynthetic pathway comprising the following substrate to product conversions: pyruvate to acetolactate, acetolactate to 2,3-dihydroxyisovalerate, 2,3-dihydroxyisovalerate to α-ketoisovalerate, α-ketoisovalerate to valine, valine to isobutylamine, isobutylamine to isobutyraldehyde, and isobutyraldehyde to isobutanol; a 1-butanol biosynthetic pathway comprising the following substrate to product conversions: acetyl-CoA to acetoacetyl-CoA, acetoacetyl-CoA to 3-hydroxybutyryl-CoA, 3-hydroxybutyryl-CoA to crotonyl-CoA, crotonyl-CoA to butyryl-CoA, butyryl-CoA to butyraldehyde, and butyraldehyde to 1-butanol; a 2-butanol biosynthetic pathway comprising the following substrate to product conversions: pyruvate to alpha-acetolactate, alpha-acetolactate to acetoin, acetoin to 2,3-butanediol, 2,3-butanediol to 2-butanone, and 2-butanone to 2-butanol. In embodiments, the yield of butanol in the butanol and fusel oil mixture is increased. In embodiments, the yield of fusel oil in the butanol and fusel oil mixture is increased. In embodiments, the saccharifying and the fermenting occur in the same vessel. In embodiments, the saccharifying and the fermenting occur concurrently.

BRIEF DESCRIPTION OF THE FIGURES AND SEQUENCE DESCRIPTIONS

The invention can be more fully understood from the following detailed description, the Figures, and the accompanying sequence descriptions, which form part of this application.

FIG. 1, illustrates the Ehrlich pathway, wherein branched-chain amino acids (i.e., leucine, valine and isoleucine), aromatic amino acids (i.e., phenyl-alanine, tyrosine and tryptophan) and a sulfur-containing amino acid (i.e., methionine) lead to the formation of fusel acids and fusel alcohols. Genes encoding enzymes for each step are indicated.

FIG. 2 schematically shows a portion of the Saccharomyces cerevisiae pathway for degradation of: (A) valine; and, (B) isoleucine.

FIG. 3 schematically shows a portion of the Saccharomyces cerevisiae pathway for degradation of: (A) leucine; and, (B) tyrosine.

FIG. 4 schematically shows a portion of the Saccharomyces cerevisiae pathway for degradation of: (A) phenylalanine; and, (B) tryptophan.

FIG. 5 schematically illustrates example methods and systems of the present invention, in which: (A) undissolved solids are removed in a centrifuge after liquefaction and before fermentation; or (B) feedstock is milled.

FIG. 6 schematically illustrates example methods and systems of the present invention, in which: (A) the centrifuge discharges an oil stream; or (B) a saccharification vessel is placed between the centrifuge and the fermentor.

FIG. 7 schematically illustrates alternative exemplary methods and systems of the present invention, in which: (A) a saccharification vessel is placed between the liquefaction vessel and the centrifuge; or (B) two centrifuges are utilized in series to remove the undissolved solids.

FIG. 8 shows different isobutanol biosynthetic pathways. The steps labeled “a,” “b,” “c,” “d,” “e,” “f,” “g,” “h,” “I,” “j,” and “k” represent the substrate to product conversions described herein. Step “a” may be catalyzed, for example, by acetolactate synthase. Step “b” may be catalyzed, for example, by acetohydroxy acid isomeroreductase. Step “c” may be catalyzed, for example, by acetohydroxy acid dehydratase. Step “d” may be catalyzed, for example, by branched-chain keto acid decarboxylase. Step “e” may be catalyzed, for example, by branched chain alcohol dehydrogenase. Step “f” may be catalyzed, for example, by branched chain keto acid dehydrogenase. Step “g” may be catalyzed, for example, by an acetylating aldehyde dehydrogenase. Step “h” may be catalyzed, for example, by a transaminase. Step “i” may be catalyzed, for example, by a valine decarboxylase. Step “j” may be catalyzed, for example, by an omega transaminase.

FIG. 9 shows four different pathways for biosynthesis of 1-butanone and 1-butanol. The steps labeled “a,” “b,” “c,” “d,” “e,” and “f” represent the substrate to product conversions described herein. Step “a” may be catalyzed, for example, by acetyl-CoA acetyl transferase. Step “b” may be catalyzed, for example, by 3-hydroxybutyryl-CoA dehydrogenase. Step “c” may be catalyzed, for example, by crotonase. Step “d” may be catalyzed, for example, by butyryl-CoA dehydrogenase. Step “e” may be catalyzed, for example, by butyraldehyde dehydrogenase. Step “f” may be catalyzed, for example, by butanol dehydrogenase.

FIG. 10 shows four different pathways for biosynthesis of 2-butanone and 2-butanol. The steps labeled “a,” “b,” “c,” “d,” “e,” “f,” “g,” “h,” “I,” “j,” “k,” “l,” and “m” represent the substrate to product conversions described herein. Step “a” may be catalyzed, for example, by acetolactate synthase. Step “b” may be catalyzed, for example, by acetolactate decarboxylase. Step “c” may be catalyzed, for example, by acetoin aminase. Step “d” may be catalyzed, for example, by aminobutanol kinase. Step “e” may be catalyzed, for example, by aminobutanol phosphate phospho-lyase. Step “f” may be catalyzed, for example, by butanol dehydrogenase. Step “g” may be catalyzed, for example, by a dihydroxyacetone kinase. Step “h” may be catalyzed, for example, by a serinol phosphate aminotransferase. Step “i” may be catalyzed, for example, by a butanediol dehydrogenase. Step “j” may be catalyzed, for example, by a diol dehydratase or glycerol dehydratase.

FIG. 11 depicts a biosynthetic production matrix comprising an isobutanol production pathway, a 3-methyl-1-butanol production pathway, a 2-methyl-1-butanol pathway and a 1-propanol production pathway. The steps catalyzed by LEU4/9 and ILV1 are indicated as branchpoints for production of 3-methyl-1-butanol and 2-methyl-1-butanol/1-propanol, respectively, in the biosynthetic production matrix.

FIG. 12 shows an example alcohol production process. Streams which may contain hydrolysable proteins are depicted with an asterisk.

TABLE 1 Summary of Gene and Protein SEQ ID Numbers Protein DNA SEQ SEQ ID Gene ID NO NO Saccharomyces cerevisiae Aromatic aminotransferase I  1  2 (GenBank Accession No. NM_001181067) (“ARO8”) (1503 bp) (500 AA) Saccharomyces cerevisiae Aromatic aminotransferase II  3  4 (GenBank Accession No. NM_001179267) (“ARO9”) (1542 bp) (513 AA) Saccharomyces cerevisiae Phenyl pyruvate decarboxylase  5  6 (GenBank Accession No. NM_001180688) (“ARO10”) (1908 bp) (635 AA) Saccharomyces cerevisiae Mitochondrial branched chain  7  8 amino acid transferase (GenBank Accession No. X78961) (1835 bp) (393 AA) (“BAT1”) Saccharomyces cerevisiae Cytosolic branched chain amino  9 10 acid transferase (GenBank Accession No. NM_001181806) (1131 bp) (376 AA) (“BAT2”) Saccharomyces cerevisiae Pyruvate decarboxylase 11 12 (GenBank Accession No. NM_001181931) (“PDC1”) (1692 bp) (563 AA) Saccharomyces cerevisiae Pyruvate decarboxylase 13 14 (GenBank Accession No. NM_001182021) (“PDC5”) (1692 bp) (563 AA) Saccharomyces cerevisiae Pyruvate decarboxylase 15 16 (GenBank Accession No. NM_001181216) (“PDC6”) (1692 bp) (563 AA) Saccharomyces cerevisiae Alpha-ketoisocaproate 17 18 decarboxylase (“THI3”) (GenBank Accession No. D21880) (3169 bp) (568 AA) Saccharomyces cerevisiae Alcohol dehydrogenase 19 20 (GenBank Accession No. V01291) (“ADH1”) (360 bp) (120 AA) Saccharomyces cerevisiae Alcohol dehydrogenase 21 22 (GenBank Accession No. NM_001182812) (“ADH2”) (1047 bp) (348 AA) Saccharomyces cerevisiae Alcohol dehydrogenase 23 24 (GenBank Accession No. NM_001182582) (“ADH3”) (1128 bp) (375 AA) Saccharomyces cerevisiae Alcohol dehydrogenase 25 26 (GenBank Accession No. X05992) (“ADH4”) (2160 bp) (382 AA) Saccharomyces cerevisiae Alcohol dehydrogenase 27 28 (GenBank Accession No. NM_001178493) (“ADH5”) (1056 bp) (351 AA) Saccharomyces cerevisiae Alcohol dehydrogenase 29 30 (GenBank Accession No. NM_001182831) (“ADH6”) (1083 bp) (360 AA) Saccharomyces cerevisiae Alcohol dehydrogenase (class III) 31 32 (GenBank Accession No. NM_001180228) (“SFA1”) (1161 bp) (386 AA) Saccharomyces cerevisiae Putative aryl-alcohol 33 34 dehydrogenase (1092 bp) (363 AA) (GenBank Accession No. NM_001178814) (“AAD3”) Saccharomyces cerevisiae Putative aryl-alcohol 35 36 dehydrogenase  (990 bp) (329 AA) (GenBank Accession No. NM_001180303) (“AAD4”) Saccharomyces cerevisiae Putative aryl-alcohol 37 38 dehydrogenase  (639 bp) (212 AA) (GenBank Accession No. NM_001179911) (“AAD6”) Saccharomyces cerevisiae Putative aryl-alcohol 39 40 dehydrogenase  (867 bp) (288 AA) (GenBank Accession No. NM_001181813) (“AAD10”) Saccharomyces cerevisiae Putative aryl-alcohol 41 42 dehydrogenase (1131 bp) (376 AA) (GenBank Accession No. NM_001183169) (“AAD14”) Saccharomyces cerevisiae Putative aryl-alcohol 43 44 dehydrogenase  (432 bp) (143 AA) (GenBank Accession No. NM_001183418) (“AAD15”) Saccharomyces cerevisiae Putative aryl-alcohol 45 46 dehydrogenase (GenBank Accession No. NM_001179910)  (459 bp) (152 AA) (“AAD16”) Saccharomyces cerevisiae Putative aryl-alcohol 47 48 dehydrogenase (GenBank Accession No. NM_001183902) (1029 bp) (342 AA) (“YPL088W”) Saccharomyces cerevisiae ATP-binding ATP transporter 49 50 (GenBank Accession No. NM_001183872) (“PDR12”) (4536 bp) (1511 AA) Saccharomyces cerevisiae Aldehyde dehydrogenase 51 52 (GenBank Accession No. NM_001182674) (“ALD2”) (1521 bp) (506 AA) Saccharomyces cerevisiae Aldehyde dehydrogenase 53 54 (GenBank Accession No. NM_001182673) (“ALD3”) (1521 bp) (506 AA) Saccharomyces cerevisiae Aldehyde dehydrogenase 55 56 (GenBank Accession No. NM_001183794) (“ALD4”) (1560 bp) (519 AA) Saccharomyces cerevisiae Aldehyde dehydrogenase 57 58 (GenBank Accession No. NM_001178964) (“ALD5”) (1563 bp) (520 AA) Saccharomyces cerevisiae Aldehyde dehydrogenase 59 60 (GenBank Accession No. NM_001183875) (“ALD6”) (1503 bp) (500 AA) Plasmid pLA54 61 — (4519 bp) Primers BK505 and BK506 62-63 — Primers LA468 and LA492 64-65 — Primers AK109-1, AK109-2, and AK109-3 66-68 — Primers oBP452, oBP453, oBP454, oBP455, oBP456, 69-80 — oBP457, oBP458, oBP459, oBP460,, LA135, oBP461 and LA92 Plasmid pLA59 81 — (4242 bp) Primers LA678, LA679, LA337, LA692 and LA693 82-86 — Plasmid pLA34 87 — (7523 bp) Primers LA722, LA733, LA453, LA694 and LA695 88-92 — Primers oBP594, oBP595, oBP596, oBP597, oBP598,  93-102 — oBP599, oBP600, oBP601, oBP602, and oBP603 2-micron plasmid fragments LA811 and LA817 103-104 — 2-micron plasmid fragments LA812 and LA818 105-106 — Primers LA512, LA513, LA516, LA514 and LA515 107-111 — Plasmid pLA71 112  — (6903 bp) Primers LA829, LA834, N1257, LA830 113-116 — Plasmid pLA59::FBA1p-BAT1-CYC1t 117  — (6369 bp) Plasmid pLA59::FBA1p-BAT2-CYC1t 118  — (6318 bp) Plasmid pLA59::TDH3p-ARO8-ADH1t 119  — (6682 bp) Plasmid pLA59::TDH3p-ARO9-ADHt1 120  — (6721 bp) Plasmid pLA59::TDH3p-ARO10-ADH1t 121  — (7087 bp) Plasmid pHR81-ILV5p-K9SB2 122  — (9613 bp) Plasmid pLA84 123 — (13022 bp)  Anaerostipes caccae ketol-acid reductoisomerase, variant — 124  K9SB2 (343 AA) Streptococcus mutans dihydroxyacid dehydratase (ilvD) 125  126  (1713 bp) (571 AA) Listeria grayi branched-chain α-keto acid decarboxylase (kivD) 127  128  (1647 bp) (548 AA) Beijerinckia indica alcohol dehydrogenase (ADH) — 129  (347 AA) Lactococcus lactis dihydroxyacid dehydratase 130 131  (1713 bp) (570 AA) Macrococcus caseolyticus 2-ketoisovalerate decarboxylase 132  133  (1641 bp) (546 AA) Achromobacter xylosoxidans alcohol dehydrogenase — 134  (348 AA) Bacillus subtilis AlsS — 135  (571 AA) Escherichia coli ketol-acid reductoisomerase — 136 (491 AA) Pseudomonas fluorescens ketol-acid reductoisomerase — 137  (338 AA)

DETAILED DESCRIPTION

The Applicants have provided herein processes and recombinant microorganisms which permit improved yields of fermentation products by capitalizing on both carbohydrates and amino acids present in feedstocks. While recombinant host cells capable of converting carbohydrates to butanol have been described (see, for example, U.S. Pat. No. 7,851,188, incorporated herein by reference), the present application describes processes and recombinant microorganisms which may be employed to provide increased production of butanol and/or fusel alcohols. For some purposes, it may be desirable to minimize non-isobutanol fusels to increase yield of isobutanol, while for other purposes, it may be desirable to maximize production of a particular non-isobutanol fusel alcohol or a subset of non-isobutanol fusel alcohols in conjunction with production of butanol. Equipped with this specification, one of skill in the art will be able to employ the appropriate combination of feedstock processing steps and recombinant microorganism to produce the desired combination of fermentation product alcohols.

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. In case of conflict, the present application including the definitions will control. Also, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. All publications, patents and other references mentioned in this specification are indicative of the level of skill of those skilled in the art to which this invention pertains, and are herein incorporated by reference in their entireties for all purposes to the same extent whether or not each individual publication or patent application is specifically and individually indicated to be incorporated by reference, unless only specific sections of patents or patent publications are indicated to be incorporated by reference.

Although methods and materials similar or equivalent to those disclosed herein can be used in practice or testing of the present invention, suitable methods and materials are disclosed below. The materials, methods and examples are illustrative only and are not intended to be limiting. Other features and advantages of the invention will be apparent from the detailed description and from the claims.

In order to further define this invention, the following terms, abbreviations and definitions are herein provided.

As used herein, the terms “comprises,” “comprising,” “includes,” “including,” “has,” “having,” “contains,” or “containing,” or any other variation thereof, will be understood to imply the inclusion of a stated integer or group of integers but not the exclusion of any other integer or group of integers. For example, a composition, a mixture, a process, a method, an article, or an apparatus that comprises a list of elements is not necessarily limited to only those elements but can include other elements not expressly listed or inherent to such composition, mixture, process, method, article, or apparatus. Further, unless expressly stated to the contrary, “or” refers to an inclusive or and not to an exclusive or. For example, a condition A or B is satisfied by any one of the following: A is true (or present) and B is false (or not present), A is false (or not present) and B is true (or present), and both A and B are true (or present).

Also, the indefinite articles “a” and “an” preceding an element or component of the invention are intended to be nonrestrictive regarding the number of instances, that is, occurrences of the element or component. Therefore “a” or “an” should be read to include one or at least one, and the singular word form of the element or component also includes the plural unless the number is obviously meant to be singular.

The term “invention” or “present invention” as used herein is a non-limiting term and is not intended to refer to any single embodiment of the particular invention but encompasses all possible embodiments as described in the application.

As used herein, the term “about” modifying the quantity of an ingredient or reactant of the invention employed refers to variation in the numerical quantity that can occur, for example, through typical measuring and liquid handling procedures used for making concentrates or solutions in the real world; through inadvertent error in these procedures; through differences in the manufacture, source, or purity of the ingredients employed to make the compositions or to carry out the methods; and the like. The term “about” also encompasses amounts that differ due to different equilibrium conditions for a composition resulting from a particular initial mixture. Whether or not modified by the term “about,” the claims include equivalents to the quantities. In one embodiment, the term “about” means within 10% of the reported numerical value, alternatively within 5% of the reported numerical value.

“Biomass” as used herein refers to a natural product containing hydrolyzable polysaccharides that provide fermentable sugars including any sugars and starch derived from natural resources such as corn, cane, wheat, cellulosic or lignocellulosic material and materials comprising cellulose, hemicellulose, lignin, starch, oligosaccharides, disaccharides and/or monosaccharides, and mixtures thereof. Biomass may also comprise additional components such as protein and/or lipids. Biomass may be derived from a single source or biomass can comprise a mixture derived from more than one source. For example, biomass may comprise a mixture of corn cobs and corn stover, or a mixture of grass and leaves. Biomass includes, but is not limited to, bioenergy crops, agricultural residues, municipal solid waste, industrial solid waste, sludge from paper manufacture, yard waste, waste sugars, wood and forestry waste. Examples of biomass include, but are not limited to, corn grain, corn cobs, crop residues such as corn husks, corn stover, grasses, wheat, rye, wheat straw, barley, barley straw, hay, rice straw, switchgrass, waste paper, sugar cane bagasse, sorghum, sugar cane, soy, components obtained from milling of grains, trees, branches, roots, leaves, wood chips, sawdust, shrubs and bushes, vegetables, fruits, flowers, animal manure, and mixtures thereof. For example, mash, juice, molasses, or hydrolysate may be formed from biomass by any processing known in the art for processing the biomass for purposes of fermentation such as by milling, treating, and/or liquefying and comprises fermentable sugar and may comprise water. For example, cellulosic and/or lignocellulosic biomass may be processed to obtain a hydrolysate containing fermentable sugars by any method known to one skilled in the art. A low ammonia pretreatment is disclosed in U.S. Patent Application Publication No. 2007/0031918A1, which is herein incorporated by reference. Enzymatic saccharification of cellulosic and/or lignocellulosic biomass typically makes use of an enzyme consortium for breaking down cellulose and hemicellulose to produce a hydrolysate containing sugars including glucose, xylose, and arabinose. (Saccharification enzymes suitable for cellulosic and/or lignocellulosic biomass are reviewed in Lynd, et al. (Microbiol. Mol. Biol. Rev. 66:506-577, 2002).

Mash, juice, molasses, or hydrolysate may include feedstock 12 and feedstock slurry 16 as described herein. An aqueous feedstream may be derived or formed from biomass by any processing known in the art for processing the biomass for purposes of fermentation such as by milling, treating, and/or liquefying and comprises fermentable carbon substrate (e.g., sugar) and may comprise water. An aqueous feedstream may include feedstock 12 and feedstock slurry 16 as described herein.

“Feedstock” as used herein means a feed in a fermentation process, the feed containing a fermentable carbon source with or without undissolved solids, and where applicable, the feed containing the fermentable carbon source before or after the fermentable carbon source has been liberated from starch or obtained from the break down of complex sugars by further processing such as by liquefaction, saccharification, or other process. Feedstock includes or is derived from a biomass. Suitable feedstocks include, but are not limited to, rye, wheat, corn, corn mash, cane, cane mash, barley, cellulosic material, lignocellulosic material, or mixtures thereof. Where reference is made to “feedstock oil,” it will be appreciated that the term encompasses the oil produced from a given feedstock.

“Processed feedstock slurry” refers to a slurry comprising feedstock that has been processed in a manner to produce protein hydrolysates and fermentable carbohydrate substrate. This processing will typically comprises steps resulting in liquefaction, saccharification and protein hydrolysis.

“Renewable hydrocarbon composition comprising butanol” as used herein refers to the butanol and fusel oil mixture produced from biomass by the action of microorganisms during fermentation.

“Fermentation medium” as used herein means the mixture of water, sugars, dissolved solids, optionally microorganisms producing alcohol, product alcohol, and all other constituents of the material held in the fermentation vessel in which product alcohol is being made by the reaction of sugars to alcohol, water, and carbon dioxide (CO₂) by the microorganisms present. From time to time, as used herein the term “fermentation broth” and “fermented mixture” can be used synonymously with “fermentation medium.”

“Fermentable carbon source” or “fermentable carbon substrate” as used herein means a carbon source capable of being metabolized by the microorganisms disclosed herein for the production of fermentative alcohol. Suitable fermentable carbon sources include, but are not limited to, monosaccharides such as glucose or fructose; disaccharides such as lactose or sucrose; oligosaccharides; polysaccharides such as starch or cellulose; C5 sugars such as xylose and arabinose; one carbon substrates including methane; and mixtures thereof.

“Fermentable sugar” as used herein refers to one or more sugars capable of being metabolized by the microorganisms disclosed herein for the production of fermentative alcohol.

“Fermentation vessel” as used herein means the vessel in which the fermentation reaction is carried out whereby product alcohol such as butanol is made from sugars.

“Liquefaction vessel” as used herein means the vessel in which liquefaction is carried out. Liquefaction is the process in which oligosaccharides are liberated from the feedstock. In some embodiments where the feedstock is corn, oligosaccharides are liberated from the corn starch content during liquefaction.

“Saccharification vessel” as used herein means the vessel in which saccharification (i.e., the breakdown of oligosaccharides into monosaccharides) is carried out. Where fermentation and saccharification occur simultaneously, the saccharification vessel and the fermentation vessel may be one in the same vessel.

“Sugar” as used herein refers to oligosaccharides, disaccharides, monosaccharides, and/or mixtures thereof. The term “saccharide” also includes carbohydrates including starches, dextrans, glycogens, cellulose, pentosans, as well as sugars.

As used herein, “saccharification enzyme” means one or more enzymes that are capable of hydrolyzing polysaccharides and/or oligosaccharides, for example, alpha-1,4-glucosidic bonds of glycogen, or starch. Saccharification enzymes may include enzymes capable of hydrolyzing cellulosic or lignocellulosic materials as well.

“Undissolved solids” as used herein means non-fermentable portions of feedstock, for example, germ, fiber, and gluten. For example, the non-fermentable portions of feedstock include the portion of feedstock that remains as solids and can absorb liquid from the fermentation broth.

Dried Distillers' Grains with Solubles (DDGS) as used herein refers to a co-product or by-product from a fermentation of a feedstock or biomass (e.g., fermentation of grain or grain mixture that produces a product alcohol). In some embodiments, DDGS may also refer to an animal feed product produced from a process of making a product alcohol (e.g., butanol, isobutanol, etc.).

“Product alcohol” as used herein refers to any alcohol that can be produced by a microorganism in a fermentation process that utilizes biomass as a source of fermentable carbon substrate. Product alcohols include, but are not limited to, C₁ to C₈ alkyl alcohols. In some embodiments, the product alcohols are C₂ to C₈ alkyl alcohols. In some embodiments, the product alcohols are C₃ to C₈ alkyl alcohols. In other embodiments, the product alcohols are C₂ to C₅ alkyl alcohols. In other embodiments, the product alcohols are C₃ to C₅ alkyl alcohols. It will be appreciated that C₁ to C₈ alkyl alcohols include, but are not limited to, methanol, ethanol, propanol, butanol, and pentanol. Likewise C₂ to C₈ alkyl alcohols include, but are not limited to, ethanol, propanol, butanol, and pentanol. “Alcohol” is also used herein with reference to a product alcohol.

“Butanol” as used herein refers with specificity to the butanol isomers 1-butanol (1-BuOH), 2-butanol (2-BuOH), tert-butanol (t-BuOH), and/or isobutanol (iBuOH or i-BuOH or I-BUOH, also known as 2-methyl-1-propanol), either individually or as mixtures thereof. From time to time, when referring to esters of butanol, the terms “butyl esters” and “butanol esters” may be used interchangeably.

The term “fusel alcohols” refers to aliphatic and aromatic alcohols comprising more than two carbon atoms that are formed by fermentation with yeast and are components of “fusel oils,” As used herein, “fusel alcohols” refer to isobutanol, 2-methyl-1-butanol, 3-methyl-1-butanol, 2-phenylethanol, and 1-propanol. Fusel alcohols are derived from amino acid catabolism via a pathway that was first proposed a century ago by F. Ehrlich (Über die Bedingungen der Fuselölbildung Lind über ihren Zusammenhang mit dem Eiweissaufbau der Hefe. Ber, Dtsch. Chem. Ges. 40:1027-1047, 1907). Amino acids that are assimilated by the Ehrlich pathway (i.e., valine, leucine, isoleucine, methionine, and phenylalanine) are initially transaminated, and the resulting α-keto acid cannot be redirected into central carbon metabolism. Thus, these α-keto acids may be converted into fusel alcohols or acids via the Ehrlich pathway (see FIG. 1; Hazelwood, et al., Appl. Environ. Microbiol. 74(8):2259-2266, 2008). “Non-isobutanol fusel alcohols” refers to the fusel alcohols independent of isobutanol.

The term “separation” as used herein is synonymous with “recovery” and refers to removing a chemical compound from an initial mixture to obtain the compound in greater purity or at a higher concentration than the purity or concentration of the compound in the initial mixture.

The term “yield” refers to the amount of product per amount of biomass source in g/kg. While determinations of yield often only consider the available carbon (e.g., glucose) in the biomass source, in the present invention, yield is based on the available energy that can be extracted from both carbon (e.g., glucose) and nitrogen (e.g., amino acids) containing compounds in the biomass. The yield may be exemplified for corn as the biomass source. It is understood unless otherwise noted that yield is expressed as a percentage of the theoretical yield. In reference to a microorganism or metabolic pathway, “theoretical yield” is defined as the maximum amount of product that can be generated per total amount of substrate as dictated by the stoichiometry of the metabolic pathway used to make the product. For example, the theoretical yield for one typical conversion of glucose to isopropanol is 0.33 g/g. As such, a yield of isopropanol from glucose of 0.297 g/g would be expressed as 90% of theoretical or 90% theoretical yield. One skilled in the art will appreciate that the yield may vary depending on the biomass source used. One skilled in the art can calculate yields on various biomass sources.

As used herein, “recombinant microorganism” refers to microorganisms, such as bacteria or yeast, that are modified by use of recombinant DNA techniques, such as by engineering a host cell to comprise a biosynthetic pathway such as butanol. For example, a recombinant host cell comprising an “engineered alcohol production pathway” (such as an engineered butanol or isobutanol production pathway) refers to a host cell containing a modified pathway that produces alcohol in a manner different than that normally present in the host cell. Such differences include production of an alcohol not typically produced by the host cell, or increased or more efficient production.

The term “butanologen” as used herein refers to a microorganism capable of producing a butanol isomer. Such microorganisms are typically recombinant microorganisms comprising an engineered butanol biosynthetic pathway. The term “isobutanologen” as used herein refers to a microorganism capable of producing isobutanol isomers. Such microorganisms are typically recombinant microorganisms comprising an engineered isobutanol biosynthetic pathway.

The term “butanol biosynthetic pathway” as used herein refers to an enzyme pathway to produce 1-butanol, 2-butanol, or isobutanol.

The term “1-butanol biosynthetic pathway” as used herein refers to an enzyme pathway to produce 1-butanol from acetyl-coenzyme A (acetyl-CoA).

The term “2-butanol biosynthetic pathway” as used herein refers to an enzyme pathway to produce 2-butanol from pyruvate.

The term “isobutanol biosynthetic pathway” as used herein refers to an enzyme pathway to produce isobutanol from pyruvate. For example, isobutanol biosynthetic pathways are disclosed in U.S. Pat. No. 7,851,188, which is incorporated by reference herein. Certain isobutanol biosynthetic pathways are illustrated in FIG. 1 and described herein. Isobutanol is also known as 2-methyl-1-propanol.

The term “Ehrlich pathway” refers to a pathway for catabolism of branched-chain amino acids, aromatic amino acids and the sulfur containing amino acid, as first proposed a century ago by F. Ehrlich (supra). As used herein, “Ehrlich pathway gene” refers to any gene encoding a polypeptide that catalyzes a reaction of the Ehrlich pathway, i.e., transamination (e.g., ARO8, ARO9, BAT1, BAT2), decarboxylation (e.g., ARO10, THI3, PDC1, PDC5, PDC6), oxidation (e.g., ALD1, ALD2, ALD3, ALD4, ALD5, ALD6), reduction (e.g., ADH1, ADH2, ADH3, ADH4, ADH5, ADH6, SFA1, AAD3, AAD4, AAD6, AAD10, AAD14, AAD15, AAD16, YPL088W) and export (e.g., PDR12) for production of fusel oil (see FIG. 1; Hazelwood, et al., Appl. Environ. Microbiol. 74(8):2259-2266, 2008). Sequences encoding ARO8, ARO9, BAT1, BAT2, ARO10, PDC1, PDC5, PDC6, ALD1, ALD2, ALD3, ALD4, ALD5, ALD6, THI3, ADH1, ADH2, ADH3, ADH4, ADH5, ADH6, SFA1, AAD3, AAD4, AAD6, AAD10, AAD14, AAD15, AAD16, YPL088W and PDR12 are available in the art from a variety of yeast; for example, the sequences encoding these Ehrlich pathway genes from Saccharomyces cerevisiae are provided herein as SEQ ID NOs:1-60, although the invention is by no means limited thereto.

The term “heterologous biosynthetic pathway” as used herein refers to an enzyme pathway to produce a product in which at least one of the enzymes is not endogenous to the host cell containing the biosynthetic pathway.

The term “biosynthetic production matrix” as used herein refers to a network of production pathways introduced in the cell by heterologous expression of at least two, at least three, at least four, or all of α-ketoisovalerate decarboxylase, alcohol dehydrogenase, acetolactate synthase, ketol-acid reductoisomerase, and dihydroxyacid dehydratase. As shown in FIG. 11, a biosynthetic production matrix so engineered is capable of production of isobutanol, 2-methyl-1-butanol, 3-methyl-1-butanol, 1-propanol, or combinations thereof.

The term “production matrix branchpoint” as used herein refers to the pathway steps wherein more than one product can be produced depending on the enzyme catalyzing the substrate to product conversion. For example, in FIG. 11, α-ketoisovalerate may be converted to either isobutyraldehyde or 2-isopropylmalate. Thus, such point in the matrix is a production matrix branchpoint.

The term “production matrix branchpoint enzyme” as used herein refers to the endogenous pathway enzymes which may be targeted to increase or decrease activity, ultimately resulting in increased or decreased production of a given matrix product. For example, in FIG. 11, alteration of LEU4 or LEU9 activity would so alter 2-methyl-1-butanol production. Likewise, alteration of ILV1 activity would alter production of 1-propanol and 3-methyl-1-butanol.

Polypeptides and Polynucleotides for Use in the Invention

The term “polypeptide” is intended to encompass a singular “polypeptide” as well as plural “polypeptides,” and refers to a molecule composed of monomers (amino acids) linearly linked by amide bonds (also known as peptide bonds). The term “polypeptide” refers to any chain or chains of two or more amino acids, and does not refer to a specific length of the product. Thus, “peptides,” “dipeptides,” “tripeptides,” “oligopeptides,” “protein,” “amino acid chain” or any other term used to refer to a chain or chains of two or more amino acids, are included within the definition of “polypeptide,” and the term “polypeptide” may be used instead of, or interchangeably with any of these terms. A polypeptide may be derived from a natural biological source or produced by recombinant technology, but is not necessarily translated from a designated nucleic acid sequence. It may be generated in any manner, including by chemical synthesis. The polypeptides used in this invention comprise full-length polypeptides and fragments thereof.

The term “polynucleotide” is intended to encompass a singular nucleic acid as well as plural nucleic acids, and refers to a nucleic acid molecule or construct, for example, messenger RNA (mRNA) or plasmid DNA (pDNA). As used herein, a “gene” is a polynucleotide. A polynucleotide can contain the nucleotide sequence of the full-length cDNA sequence or a fragment thereof, including the untranslated 5′ and 3′ sequences and the coding sequences. The polynucleotide can be composed of any polyribonucleotide or polydeoxyribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA (e.g., heterologous DNA). For example, polynucleotides can be composed of single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or a mixture of single- and double-stranded regions. “Polynucleotide” embraces chemically, enzymatically, or metabolically modified forms.

A polynucleotide sequence may be referred to as “isolated,” in which it has been removed from its native environment. For example, a heterologous polynucleotide encoding a polypeptide or polypeptide fragment having dihydroxy-acid dehydratase activity contained in a vector is considered isolated for the purposes herein. Further examples of an isolated polynucleotide include recombinant polynucleotides maintained in heterologous host cells or purified (partially or substantially) polynucleotides in solution. Isolated polynucleotides or nucleic acids according to the present invention further include such molecules produced synthetically. An isolated polynucleotide fragment in the form of a polymer of DNA may be comprised of one or more segments of cDNA, genomic DNA, or synthetic DNA.

By an “isolated” polypeptide or a fragment, variant, or derivative thereof is intended a polypeptide that is not in its natural milieu. No particular level of purification is required. For example, an isolated polypeptide can be removed from its native or natural environment. Recombinantly produced polypeptides and proteins expressed in host cells are considered isolated for purposes of the invention, as are native or recombinant polypeptides which have been separated, fractionated, or partially or substantially purified by any suitable technique.

As used herein, “native” refers to the form of a polynucleotide, gene, or polypeptide as found in nature with its own regulatory sequences, if present.

The term “endogenous,” when used in reference to a polynucleotide, a gene, or a polypeptide refers to a native polynucleotide or gene in its natural location in the genome of an organism, or for a native polypeptide, is transcribed and translated from this location in the genome.

The term “heterologous” when used in reference to a polynucleotide, a gene, or a polypeptide refers to a polynucleotide, gene, or polypeptide not normally found in the host organism or is found natively but is modified in some way as compared to its native state. “Heterologous” also includes a native coding region, or portion thereof, that is reintroduced into the source organism in a form that is different from the corresponding native gene, e.g., not in its natural location in the organism's genome. The heterologous polynucleotide or gene may be introduced into the host organism by, e.g., gene transfer. A heterologous gene may include a native coding region with non-native regulatory regions that is reintroduced into the native host. A “transgene” is a gene that has been introduced into the genome by a transformation procedure.

The term “gene” refers to a nucleic acid fragment that is capable of being expressed as a specific protein, optionally including regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence. “Native gene” refers to a gene as found in nature with its own regulatory sequences. “Chimeric gene” refers to any gene that is not a native gene (i.e., it is modified from its native state or is from another source) comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. “Endogenous gene” refers to a native gene in its natural location in the genome of an organism. A “foreign gene” or “heterologous gene” refers to a gene not normally found as a native gene in the host organism, but that is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non-native organism or chimeric genes.

As used herein, a “coding region” refers to a DNA sequence that codes for a specific amino acid sequence. Although a “stop codon” (TAG, TGA, or TAA) is not translated into an amino acid, it may be considered to be part of a coding region, if present, but any flanking sequences, for example promoters, ribosome binding sites, transcriptional terminators, introns, 5′ and 3′ non-translated regions, and the like, are not part of a coding region.

“Regulatory sequences” refer to nucleotide sequences located upstream (5′ non-coding sequences), within, or downstream (3′ non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences can include promoters, enhancers, operators, repressors, transcription termination signals, translation leader sequences, introns, polyadenylation recognition sequences, RNA processing sites, effector binding sites and stem-loop structures.

The term “promoter” refers to a nucleic acid sequence capable of controlling the expression of a coding sequence or functional RNA. In general, a coding sequence is located 3′ to a promoter sequence. Promoters can be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic nucleic acid segments. It is understood by those skilled in the art that different promoters can direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental or physiological conditions. Promoters which cause a gene to be expressed in most cell types at most times are commonly referred to as “constitutive promoters.” “Inducible promoters,” on the other hand, cause a gene to be expressed when the promoter is induced or turned on by a promoter-specific signal or molecule. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of different lengths can have identical promoter activity. For example, it will be understood that “FBA1 promoter” can be used to refer to a fragment derived from the promoter region of the FBA1 gene.

The term “terminator” as used herein refers to DNA sequences located downstream of a coding sequence. This includes polyadenylation recognition sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression. The polyadenylation signal is usually characterized by affecting the addition of polyadenylic acid tracts to the 3′ end of the mRNA precursor. The 3′ region can influence the transcription, RNA processing or stability, or translation of the associated coding sequence. It is recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of different lengths can have identical terminator activity. For example, it will be understood that “CYC1 terminator” can be used to refer to a fragment derived from the terminator region of the CYC1 gene.

The term “operably linked” refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of effecting the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in sense or antisense orientation.

The term “recombinant genetic expression element” refers to a nucleic acid fragment that expresses one or more specific proteins, including regulatory sequences preceding (5′ non-coding sequences) and following (3′ termination sequences) coding sequences for the proteins. A chimeric gene is a recombinant genetic expression element. The coding regions of an operon can form a recombinant genetic expression element, along with an operably linked promoter and termination region.

The term “expression,” as used herein, refers to the transcription and stable accumulation of sense (mRNA) or antisense RNA derived from a particular nucleic acid fragment. Expression may also refer to translation of mRNA into a polypeptide. The process includes any manifestation of the functional presence of the expressed polynucleotide, gene, or polypeptide within the cell including, without limitation, gene knockdown as well as both transient expression and stable expression.

The term “overexpression” or “up-regulated” as used herein, refers to expression that is higher than endogenous expression of the same or related gene. A heterologous gene is overexpressed if its expression is higher than that of a comparable endogenous gene. Thus, the term overexpression refers to an increase in the level of nucleic acid or protein in a host cell. Overexpression can result from increasing the level of transcription or translation of an endogenous sequence in a host cell or can result from the introduction of a heterologous sequence into a host cell. Overexpression can also result from increasing the stability of a nucleic acid or protein sequence. Expression or over-expression of a polypeptide in a recombinant host cell can be quantified according to any number of methods known to the skilled artisan and can be represented, e.g., by a percent of total cell protein. The percent of total protein can be an amount selected from greater than about 0.001% of total cell protein; greater than about 0.01% of total cell protein; greater than about 0.1% of total cell protein; greater than about 0.5% of total cell protein; greater than about 1.0% of total cell protein; greater than about 2.0% of total cell protein; greater than about 3% of total cell protein; greater than about 4.0% of total cell protein; greater than about 5% of total cell protein; greater than about 6.0% of total cell protein; greater than about 7.0% of total cell protein; greater than about 8.0% of total cell protein; greater than about 9.0% of total cell protein; greater than about 10% of total cell protein; or greater than about 20% of total cell protein.

The term “reduced activity” in connection with an Ehrlich pathway enzyme refers to down-regulation, whether partial or total, of the activity of at least one of the Ehrlich pathway enzymes, as compared to the activity of the wildtype Ehrlich pathway enzyme. Likewise, the term “reduced activity” in connection with a production matrix branch point enzyme refers to down-regulation, whether partial or total, of the activity of at least one of the production matrix branch point enzymes. Down-regulation may occur when a native gene has a “disruption” or “modification,” referring to an insertion, deletion, or targeted mutation within a portion of that gene, that results in e.g., a complete gene knockout such that the gene is deleted from the genome and no protein is translated or a translated subunit protein having an insertion, deletion, amino acid substitution or other targeted mutation. The location of the modification in the protein may be, for example, within the N-terminal portion of the protein or within the C-terminal portion of the protein. The modified protein will have impaired activity with respect to the protein that was not disrupted, and can be non-functional. Reduced activity in an Ehrlich pathway enzyme could also result via manipulating the upstream regulatory proteins or regulatory domains, altering a downstream protein regulated by the Ehrlich pathway enzyme, transcription and translation factors and/or signal transduction pathways or by use of sense, antisense or RNAi technology, etc. Another mechanism of reducing activity of an enzyme is introduction of a mutation that alters kinetic properties of the enzyme (e.g., reducing the affinity for a substrate, lowering the k_(cat), etc.).

The term “increased activity” with a production matrix branch point enzyme refers to up-regulation, whether partial or total, of the activity of at least one of the matrix branch point enzymes. Increased activity may occur when a gene encoding an enzyme is overexpressed or when a mutation is introduced into the gene or into a regulator of the gene resulting in increased transcription or translation of the gene or alteration of the kinetic properties of the enzyme.

The term “alters activity” refers to any of the aforementioned modifications resulting in increased activity or decreased activity of an indicated enzyme.

As used herein the term “transformation” refers to the transfer of a nucleic acid fragment into the genome of a host microorganism, resulting in genetically stable inheritance. Host microorganisms containing the transformed nucleic acid fragments are referred to as “transgenic” or “recombinant” or “transformed” microorganisms.

The terms “plasmid,” “vector,” and “cassette” refer to an extra chromosomal element often carrying genes which are not part of the central metabolism of the cell, and usually in the form of circular double-stranded DNA fragments. Such elements can be autonomously replicating sequences, genome integrating sequences, phage or nucleotide sequences, linear or circular, of a single- or double-stranded DNA or RNA, derived from any source, in which a number of nucleotide sequences have been joined or recombined into a unique construction which is capable of introducing a promoter fragment and DNA sequence for a selected gene product along with appropriate 3′ untranslated sequence into a cell.

“Transformation cassette” refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that facilitates transformation of a particular host cell.

“Expression cassette” refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that allow for enhanced expression of that gene in a foreign host.

As used herein the term “codon degeneracy” refers to the nature in the genetic code permitting variation of the nucleotide sequence without affecting the amino acid sequence of an encoded polypeptide. The skilled artisan is well aware of the “codon-bias” exhibited by a specific host cell in usage of nucleotide codons to specify a given amino acid. Therefore, when synthesizing a gene for improved expression in a host cell, it is desirable to design the gene such that its frequency of codon usage approaches the frequency of preferred codon usage of the host cell.

The term “codon-optimized” as it refers to genes or coding regions of nucleic acid molecules for transformation of various hosts, refers to the alteration of codons in the gene or coding regions of the nucleic acid molecules to reflect the typical codon usage of the host organism without altering the polypeptide encoded by the DNA. Such optimization includes replacing at least one, or more than one, or a significant number, of codons with one or more codons that are more frequently used in the genes of that organism.

A polynucleotide or nucleic acid fragment is “hybridizable” to another nucleic acid fragment, such as a cDNA, genomic DNA, or RNA molecule, when a single-stranded form of the nucleic acid fragment can anneal to the other nucleic acid fragment under the appropriate conditions of temperature and solution ionic strength. Hybridization and washing conditions are well known and exemplified in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y. (1989), particularly Chapter 11 and Table 11.1 therein (entirely incorporated herein by reference). The conditions of temperature and ionic strength determine the “stringency” of the hybridization. Stringency conditions can be adjusted to screen for moderately similar fragments (such as homologous sequences from distantly related organisms), to highly similar fragments (such as genes that duplicate functional enzymes from closely related organisms). Post hybridization washes determine stringency conditions. One set of conditions uses a series of washes starting with 6×SSC, 0.5% SDS at room temperature for 15 min, then repeated with 2×SSC, 0.5% SDS at 45° C. for 30 min, and then repeated twice with 0.2×SSC, 0.5% SDS at 50° C. for 30 min. Another set of stringent conditions uses higher temperatures in which the washes are identical to those above except for the temperature of the final two 30 min washes in 0.2×SSC, 0.5% SDS was increased to 60° C. Another set of highly stringent conditions uses two final washes in 0.1×SSC, 0.1% SDS at 65° C. An additional set of stringent conditions include hybridization at 0.1×SSC, 0.1% SDS, 65° C. and washes with 2×SSC, 0.1% SDS followed by 0.1×SSC, 0.1% SDS, for example.

Hybridization requires that the two nucleic acids contain complementary sequences, although depending on the stringency of the hybridization, mismatches between bases are possible. The appropriate stringency for hybridizing nucleic acids depends on the length of the nucleic acids and the degree of complementation, variables well known in the art. The greater the degree of similarity or homology between two nucleotide sequences, the greater the value of Tm for hybrids of nucleic acids having those sequences. The relative stability (corresponding to higher Tm) of nucleic acid hybridizations decreases in the following order: RNA:RNA, DNA:RNA, DNA:DNA. For hybrids of greater than 100 nucleotides in length, equations for calculating Tm have been derived (see Sambrook, et al., supra, 9.50 9.51). For hybridizations with shorter nucleic acids, i.e., oligonucleotides, the position of mismatches becomes more important, and the length of the oligonucleotide determines its specificity (see Sambrook, et al., supra, 11.7 11.8). In one embodiment the length for a hybridizable nucleic acid is at least about 10 nucleotides. In one embodiment, a minimum length for a hybridizable nucleic acid is at least about 15 nucleotides; at least about 20 nucleotides; or the length is at least about 30 nucleotides. Furthermore, the skilled artisan will recognize that the temperature and wash solution salt concentration can be adjusted as necessary according to factors such as length of the probe.

A “substantial portion” of an amino acid or nucleotide sequence is that portion comprising enough of the amino acid sequence of a polypeptide or the nucleotide sequence of a gene to putatively identify that polypeptide or gene, either by manual evaluation of the sequence by one skilled in the art, or by computer-automated sequence comparison and identification using algorithms such as BLAST (Altschul, et al., J. Mol. Biol. 215:403-410, 1993). In general, a sequence of ten or more contiguous amino acids or thirty or more nucleotides is necessary in order to putatively identify a polypeptide or nucleic acid sequence as homologous to a known protein or gene. Moreover, with respect to nucleotide sequences, gene specific oligonucleotide probes comprising 20-30 contiguous nucleotides can be used in sequence-dependent methods of gene identification (e.g., Southern hybridization) and isolation (e.g., in situ hybridization of bacterial colonies or bacteriophage plaques). In addition, short oligonucleotides of 12-15 bases can be used as amplification primers in PCR in order to obtain a particular nucleic acid fragment comprising the primers. Accordingly, a “substantial portion” of a nucleotide sequence comprises enough of the sequence to specifically identify and/or isolate a nucleic acid fragment comprising the sequence. The instant specification teaches the complete amino acid and nucleotide sequence encoding particular proteins. The skilled artisan, having the benefit of the sequences as reported herein, can now use all or a substantial portion of the disclosed sequences for purposes known to those skilled in this art. Accordingly, the instant invention comprises the complete sequences as reported in the accompanying Sequence Listing, as well as substantial portions of those sequences as defined above.

The term “complementary” is used to describe the relationship between nucleotide bases that are capable of hybridizing to one another. For example, with respect to DNA, adenine is complementary to thymine and cytosine is complementary to guanine, and with respect to RNA, adenine is complementary to uracil and cytosine is complementary to guanine.

The term “percent identity,” as known in the art, is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as determined by comparing the sequences. In the art, “identity” also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences. “Identity” and “similarity” can be readily calculated by known methods, including but not limited to those described in: 1.) Computational Molecular Biology (Lesk, A. M., Ed.) Oxford University: NY (1988); 2.) Biocomputing: Informatics and Genome Projects (Smith, D. W., Ed.) Academic: NY (1993); 3.) Computer Analysis of Sequence Data, Part I (Griffin, A. M., and Griffin, H. G., Eds.) Humania: NJ (1994); 4.) Sequence Analysis in Molecular Biology (von Heinje, G., Ed.) Academic (1987); and 5.) Sequence Analysis Primer (Gribskov, M. and Devereux, J., Eds.) Stockton: NY (1991).

Methods to determine identity are designed to give the best match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. Sequence alignments and percent identity calculations can be performed using the MegAlign™ program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wis.). Multiple alignments of the sequences are performed using the “Clustal method of alignment” which encompasses several varieties of the algorithm including the “Clustal V method of alignment” corresponding to the alignment method labeled Clustal V (described by Higgins and Sharp, CABIOS. 5:151-153, 1989; Higgins, et al., Comput. Appl. Biosci. 8:189-191, 1992) and found in the MegAlign™ program of the LASERGENE bioinformatics computing suite (DNASTAR Inc.). For multiple alignments, the default values correspond to GAP PENALTY=10 and GAP LENGTH PENALTY=10. Default parameters for pairwise alignments and calculation of percent identity of protein sequences using the Clustal method are KTUPLE=1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5. For nucleic acids these parameters are KTUPLE=2, GAP PENALTY=5, WINDOW=4 and DIAGONALS SAVED=4. After alignment of the sequences using the Clustal V program, it is possible to obtain a “percent identity” by viewing the “sequence distances” table in the same program. Additionally the “Clustal W method of alignment” is available and corresponds to the alignment method labeled Clustal W (described by Higgins and Sharp, CABIOS. 5:151-153 (1989); Higgins, D. G. et al., Comput. Appl. Biosci. 8:189-191 (1992)) and found in the MegAlign™ v6.1 program of the LASERGENE bioinformatics computing suite (DNASTAR Inc.). Default parameters for multiple alignment (GAP PENALTY=10, GAP LENGTH PENALTY=0.2, Delay Divergen Seqs (%)=30, DNA Transition Weight=0.5, Protein Weight Matrix=Gonnet Series, DNA Weight Matrix=IUB). After alignment of the sequences using the Clustal W program, it is possible to obtain a “percent identity” by viewing the “sequence distances” table in the same program.

It is well understood by one skilled in the art that many levels of sequence identity are useful in identifying polypeptides, such as polypeptides from other species or variants of a polypeptide, wherein such polypeptides have the same or similar function or activity, or in describing the corresponding polynucleotides. Useful examples of percent identities include, but are not limited to: 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%, or any integer percentage from 60% to 100% can be useful in describing the present invention, such as 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%. Suitable polynucleotide fragments not only have the above homologies but typically comprise a polynucleotide having at least 50 nucleotides, at least 100 nucleotides, at least 150 nucleotides, at least 200 nucleotides, or at least 250 nucleotides. Further, suitable polynucleotide fragments having the above homologies encode a polypeptide having at least 50 amino acids, at least 100 amino acids, at least 150 amino acids, at least 200 amino acids, or at least 250 amino acids.

The term “sequence analysis software” refers to any computer algorithm or software program that is useful for the analysis of nucleotide or amino acid sequences. “Sequence analysis software” can be commercially available or independently developed. Typical sequence analysis software will include, but is not limited to: 1.) the GCG suite of programs (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wis.); 2.) BLASTP, BLASTN, BLASTX (Altschul, et al., J. Mol. Biol. 215:403-410, 1990); 3.) DNASTAR (DNASTAR, Inc. Madison, Wis.); 4.) Sequencher (Gene Codes Corporation, Ann Arbor, Mich.); and 5.) the FASTA program incorporating the Smith-Waterman algorithm (W. R. Pearson, Comput. Methods Genome Res., [Proc. Int. Symp.] (1994), Meeting Date 1992, 111-20. Editor(s): Suhai, Sandor. Plenum: New York, N.Y.). Within the context of this application it will be understood that where sequence analysis software is used for analysis, that the results of the analysis will be based on the “default values” of the program referenced, unless otherwise specified. As used herein “default values” will mean any set of values or parameters that originally load with the software when first initialized.

Standard recombinant DNA and molecular cloning techniques are well known in the art and are described by Sambrook, J., Fritsch, E. F. and Maniatis, T., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989) (hereinafter “Maniatis”); and by Silhavy, T. J., Bennan, M. L. and Enquist, L. W., Experiments with Gene Fusions, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1984); and by Ausubel, F. M. et al., Current Protocols in Molecular Biology, published by Greene Publishing Assoc. and Wiley-Interscience (1987). Additional methods used here are in Methods in Enzymology, Volume 194, Guide to Yeast Genetics and Molecular and Cell Biology (Part A, 2004, Christine Guthrie and Gerald R. Fink (Eds.), Elsevier Academic Press, San Diego, Calif.).

Methods for Producing Butanol and Fusel Alcohol Mixtures in Recombinant Yeast—an Overview

Traditional recombinant fermentations utilizing various feedstocks rely on available carbon substrates to enable production of the product of interest, while various protein by-products often accumulate and are used for animal feeds. Huo, et al. (Nature Biotechnol. 29(4):346-352, 2011) suggest that a nitrogen-centric metabolic engineering strategy could be utilized to utilize proteins (versus carbon) as feedstock for the production of biofuels and they engineer an Escherichia coli that can deaminate protein hydrolysates (via introduction of three exogenous transamination and deamination cycles), enabling the cells to convert proteins to C4 and C5 alcohols (including ethanol, isobutanol, 2-methyl-1-butanol and 3-methyl-1-butanol) at 56% of the theoretical yield. Huo, et al. report that Saccharomyces cerevisiae, E. coli, Bacillus subtilis and microalgae were useful protein sources, producing up to 4,035 mg/L of alcohols from biomass containing ˜22 g/L of amino acids.

Recombinant yeast engineered to produce butanol as the primary product may co-produce fusel alcohols as minor by-products, based on pathways within the yeast and the substrates present. However, the present invention is an improvement thereof, since the yield of butanol (and optionally, the fusel alcohol) per kilogram of biomass feedstock is improved with respect to previously engineered yeast.

Specifically, the processes and/or recombinant yeast comprising butanol biosynthetic pathways herein may capitalize on both the carbon and nitrogen (via amino acids derived from the biomass protein) available in a biomass feedstock to produce butanol in a fermentation process. In one embodiment, biomass feedstock is processed such that the protein content is hydrolyzed, providing an increase in free amino acids liberated from the biomass as compared to butanol fermentation processes known in the art. In one embodiment, the excess branched chain amino acids valine, leucine, and isoleucine as well as the phenylalanine so produced are substrates for pathways in the yeast to produce fusel alcohols isobutanol, isoamyl alcohol (3-methyl-1-butanol), active amyl alcohol (2-methyl-1-butanol), and 2-phenylethanol, respectively. Increased production of one or more such fusels from previously non-utilized substrates would advantageously lead to increased yield of butanol and fusel oil mixtures per unit of biomass.

To further increase yield of hydrocarbons including butanol per unit biomass, a recombinant microorganism comprising a heterologous butanol biosynthetic pathway may be modified to utilize amino acid substrates more efficiently. In one embodiment, such modification is achieved by modification of the activity of at least one Ehrlich pathway gene (thereby affecting production of fusel alcohols). Together, the processing and host cell modifications may result in increased production of butanol and/or fusel alcohols with respect to the theoretical yield from a particular biomass feedstock, as compared to the production of butanol and/or fusel alcohols obtained from utilization of only fermentable sugars or only protein hydrolysates within the particular biomass feedstock.

Thus, in one embodiment, the present invention is drawn to a method for producing a butanol and fusel alcohol mixture from a biomass feedstock comprising:

-   -   a) providing a biomass feedstock;     -   b) processing the biomass feedstock to produce a processed         feedstock slurry comprising protein hydrolysates and         oligosaccharides;     -   c) saccharifying the oligosaccharides of the processed feedstock         slurry to produce a fermentation composition comprising         fermentable sugars and protein hydrolysates;     -   d) fermenting a recombinant yeast in the presence of the         fermentation composition, said recombinant yeast comprising:         -   (i) a heterologous butanol biosynthetic pathway for             production of butanol; and,         -   (ii) at least one upregulated Ehrlich pathway gene for             production of fusel alcohol;     -   whereby a butanol and fusel alcohol mixture is produced; and,     -   e) recovering the butanol and fusel alcohol mixture;         wherein the yield of the butanol and fusel alcohol mixture per         kilogram of biomass feedstock is increased.

Fusel Alcohol Production Pathways in Yeast

Processes for the preparation of fusel alcohols are known; see, for example, EP 624 388. Composition of fusel alcohols can vary according to the processes and according to the plant fermented.

In yeasts, under certain conditions, fusel alcohols are produced through the metabolization of nitrogenous compounds, such as amino acids. This pathway for amino acid catabolism was first proposed a century ago by F. Ehrlich (Über die Bedingungen der Fuselölbildung and über ihren Zusammenhang mit dem Eiweissaufbau der Hefe. Ber. Dtsch. Chem. Ges. 40:1027-1047, 1907). Fusel alcohols are formed by all the yeast species that have been examined (Guymon, et al., Archives of Biochemistry and Biophysics 95:163-168, 1961; Guymon, et al., American J. Enology and Viticulture 12:60-66, 1961). Hazelwood, et al. provide a useful minireview entitled “The Ehrlich Pathway for Fusel Alcohol Production: A Century of Research on Saccharomyces cerevisiae Metabolism” (Appl. Environ. Microbiol. 74(8):2259-2266, 2008). In brief, the Ehrlich Pathway is initiated by transamination of branched-chain amino acids (i.e., leucine, valine and isoleucine), aromatic amino acids (i.e., phenylalanine, tyrosine and tryptophan) and/or the sulfur-containing amino acid (i.e., methionine), which results in formation of an α-keto acid that cannot be redirected into central carbon metabolism. The α-keto acid then is decarboxylated to produce a “fusel aldehyde,” and oxidation or reduction of fusel aldehydes then occur, thereby producing fusel acids and/or fusel alcohols, respectively. These products are then either passively or actively exported from the cell into the fermentation medium.

Although the Ehrlich pathway was proposed over a century ago, experimental verification of the role of the pathway in amino acid catabolism wasn't obtained until the late 1990s, via ¹³C labeling studies. Ehrlich pathway intermediates (i.e., α-keto acids and fusel aldehydes) were confirmed. Of particular interest herein, valine is transaminated to 3-methyl-2-oxo-butanoate (“α-ketoisovalerate”), decarboxylated to 2-methylpropanal (“isobutanal” or “isovaleraldehyde”), and oxidized to produce the fusel acid 2-methylpropanoate (“isobutyrate”) or reduced to produce the fusel alcohol 2-methylpropanol (“isobutanol” or “isobutyl alcohol”) (FIG. 2A). Similarly, isoleucine is catabolized to produce 3-methyl-2-oxo-pentanoate (“α-keto-methylvalerate”), 2-methylbutanal (“methylvaleraldehyde”), the fusel acid 2-methylbutanoate (“methylvalerate”) and/or the fusel alcohol 2-methylbutanol (“active amyl alcohol”) (FIG. 2B). Leucine is transaminated to produce 4-methyl-2-oxo-pentanoate (“α-ketoisocaproate”), decarboxylated to produce 3-methylbutanal (“isoamylaldehyde”), and reduced to produce 3-methylbutanoate (“isovalerate”) or oxidized to produce 3-methylbutanol (“isoamyl alcohol”) (FIG. 3A). Tyrosine is catabolized to produce p-hydroxyphenylpyruvate, p-hydroxyphenylacetylaldehyde, the fusel acid 2-(4-hydroxyphenyl) ethanoate (“p-hydroxyphenylacetate”) and/or the fusel alcohol 2-(4-hydroxyphenyl) ethanol (“tyrosol” or “p-hydroxyphenylethanol) (FIG. 3B). Phenylalanine is transaminated to produce 3-phenyl-2-oxo-propanoate (“phenylpyruvate”), decarboxylated to produce 2-phenylethanal (“2-phenylacetaldehyde”), and reduced to produce 2-phenylethanoate (“2-phenylacetate”) or oxidized to produce 2-phenylethanol (FIG. 4A). Tryptophan is catabolized to produce 3-(indol-3-yl)-2-oxopropanoate (“3-indole pyruvate”), 2-(indol-3-yl)-2-ethanal (“3-indole acetaldehyde”), the fusel acid 2-(indol-3-yl)-2-ethanoate and/or the fusel alcohol 2-(indol-3-yl)ethanol (“tryptophol” or “indole-3-ethanol”) (FIG. 4B).

A variety of proteins play roles in the Ehrlich pathway, as shown in FIG. 1 herein and summarized in Table 2. (See Hazelwood, et al., supra.) In general, ARO8 and ARO9 are through to be minor transaminases for isoleucine and leucine catabolism, while BAT1 and BAT2 function for isoleucine, leucine and valine catabolism. ARO10 functions as a broad-substrate specificity decarboxylase for isoleucine and leucine catabolism, while PDC1, PDC5 and PDC6 typically participate in valine catabolism. Finally, recent studies with THI3 indicate that this enzyme may play a regulatory role in the Ehrlich pathway (as opposed to a catalytic role) (reviewed in Hazelwood, et al., supra).

TABLE 2 Ehrlich Pathway Proteins for Formation of Fusel Acids and Fusel Alcohols EC Enzyme Saccharomyces Reaction Enzyme Number Name cerevisiae Protein Transamination Aromatic 2.6.1.39 ARO8 GenBank Accession No. aminotransferase or NM_001181067 2.6.1.57 (SEQ ID NO: 2) Aromatic 2.6.1.57 ARO9 GenBank Accession No. aminotransferase NM_001179267 (SEQ ID NO: 4) Mitochondrial branched 2.6.1.42 BAT1 GenBank Accession No. chain amino acid X78961 transferase (SEQ ID NO: 8) Cytosolic branched chain 2.6.1.42 BAT2 GenBank Accession No. amino acid transferase NM_001181806 (SEQ ID NO: 10) Decarboxylation Phenylpyruvate 4.1.1.— ARO10 GenBank Accession No. decarboxylase NM_001180688 (SEQ ID NO: 6) Pyruvate decarboxylase 4.1.1.1 PDC1 GenBank Accession No. NM_001181931 (SEQ ID NO: 12) Pyruvate decarboxylase 4.1.1.1 PDC5 GenBank Accession No. NM_001182021 (SEQ ID NO: 14) Pyruvate decarboxylase 4.1.1.1 PDC6 GenBank Accession No. NM_001181216 (SEQ ID NO: 16) Alpha-ketoisocaproate 4.1.1.— THI3 GenBank Accession No. decarboxylase D21880 (SEQ ID NO: 18) Reduction Alcohol dehydrogenase 1.1.1.1 ADH1 GenBank Accession No. (for synthesis V01291 of fusel (SEQ ID NO: 20) alcohols) Alcohol dehydrogenase 1.1.1.1 ADH2 GenBank Accession No. NM_001182812 (SEQ ID NO: 22) Alcohol dehydrogenase 1.1.1.1 ADH3 GenBank Accession No. NM_001182582 (SEQ ID NO: 24) Alcohol dehydrogenase 1.1.1.1 ADH4 GenBank Accession No. X05992 (SEQ ID NO: 26) Alcohol dehydrogenase 1.1.1.1 ADH5 GenBank Accession No. NM_001178493 (SEQ ID NO: 28) Alcohol dehydrogenase 1.1.1.2 ADH6 GenBank Accession No. NM_001182831 (SEQ ID NO: 30) Alcohol dehydrogenase SFA1 GenBank Accession No. (class III) NM_001180228 (SEQ ID NO: 32) Putative aryl-alcohol 1.1.1.— AAD3 GenBank Accession No. dehydrogenase NM_001178814 (SEQ ID NO: 34) Putative aryl-alcohol 1.1.1.— AAD4 GenBank Accession No. dehydrogenase NM_001180303 (SEQ ID NO: 36) Putative aryl-alcohol 1.1.1.— AAD6 GenBank Accession No. dehydrogenase NM_001179911 (SEQ ID NO: 38) Putative aryl-alcohol 1.1.1.— AAD10 GenBank Accession No. dehydrogenase NM_001181813 (SEQ ID NO: 40) Putative aryl-alcohol 1.1.1.— AAD14 GenBank Accession No. dehydrogenase NM_001183169 (SEQ ID NO: 42) Putative aryl-alcohol 1.1.1.— AAD15 GenBank Accession No. dehydrogenase NM_001183418 (SEQ ID NO: 44) Putative aryl-alcohol 1.1.1.— AAD16 GenBank Accession No. dehydrogenase NM_001179910 (SEQ ID NO: 46) Putative aryl-alcohol 1.1.1.— YPL088W GenBank Accession No. dehydrogenase NM_001183902 (SEQ ID NO: 48) Oxidation Aldehyde dehydrogenase 1.2.1.5 ALD2 GenBank Accession No. (for synthesis NM_001182674 of fusel (SEQ ID NO: 52) acids) Aldehyde dehydrogenase 1.2.1.5 ALD3 GenBank Accession No. NM_001182673 (SEQ ID NO: 54) Aldehyde dehydrogenase 1.2.1.3 ALD4 GenBank Accession No. NM_001183794 (SEQ ID NO: 56) Aldehyde dehydrogenase 1.2.1.3 or ALD5 GenBank Accession No. 1.2.1.4 NM_001178964 (SEQ ID NO: 58) Aldehyde dehydrogenase 1.2.1.3 ALD6 GenBank Accession No. NM_001183875 (SEQ ID NO: 60) Export (for ATP-binding ATP — PDR12 GenBank Accession No. fusel acids) transporter NM_001183872 (SEQ ID NO: 50) Note: Suitable polypeptide sequences that encode enzymes which catalyze the reactions set forth above, as well as E.C. numbers corresponding to the substrate to product conversions indicated include, but are not limited to, those set forth above. Suitable enzymes capable of performing the substrate to product conversions associated with the given E.C. numbers will be readily available to those of skill in the art, for example, through online public databases such as the BRENDA database (http://www.brenda-enzymes.org/).

Although the Saccharomyces cerevisiae proteins shown in Table 2 are exemplary of useful Ehrlich pathway polypeptides, one of skill in the art will recognize that the present invention is not limited thereto. Thus, preferably, the polypeptide sequence encoding an Ehrlich pathway gene is selected from the group consisting of SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, and 60. In alternate embodiments, the polypeptide sequence encoding an Ehrlich pathway gene has at least 85% sequence identity based on the CLUSTALW method of alignment, when compared to any one of SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, and 60, i.e., the polypeptide may have at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity when compared thereto. In alternate embodiments, the sequences set forth in Table 2, or homologs or codon-optimized derivatives thereof, may be used in the present invention.

In other embodiments, a polynucleotide, gene and/or polypeptide encoding ARO8, ARO9, BAT1, BAT2, ARO10, PDC1, PDC5, PDC6, ALD2, ALD3, ALD4, ALD5, ALD6, THI3, ADH1, ADH2, ADH3, ADH4, ADH5, ADH6, SFA1, AAD3, AAD4, AAD6, AAD10, AAD14, AAD15, AAD16, YPL088W and PDR12 can be used to identify homologs in other cells. Such Ehrlich pathway sequences can be identified, for example, in the literature and/or in bioinformatics databases well known to the skilled person. For example, the identification of ARO8, ARO9, BAT1, BAT2, ARO10, PDC1, PDC5, PDC6, ALD1, ALD2, ALD3, ALD4, ALD5, ALD6, THI3, ADH1, ADH2, ADH3, ADH4, ADH5, ADH6, SFA1, AAD3, AAD4, AAD6, AAD10, AAD14, AAD15, AAD16, YPL088W and PDR12 encoding sequences in other cell types using bioinformatics can be accomplished through BLAST searching of publicly available databases with known Ehrlich pathway encoding DNA and polypeptide sequences, such as those provided herein as the query. Identities are based on the Clustal W method of alignment using the default parameters of GAP PENALTY=10, GAP LENGTH PENALTY=0.1, and Gonnet 250 series of protein weight matrix.

As shown in FIG. 1, only the fusel acid is exported from inside the cell (“in”) to outside in the culture medium (“out”). PDR12, an ATP-dependent transporter, has been confirmed to catalyze this active transport of the fusel acid (Hazelwood, et al., FEMS Yeast Res. 6:937-945, 2006), while fusel alcohols are thought to passively diffuse across the cells' lipid bilayer into the medium (Lipinski, Adv. Drug Deliv. Rev. 46:3-26, 2001).

It has been reported that the addition of a high concentration of valine to a fermentation medium increased Saccharomyces cerevisiae production of isobutanol, isobutyric acid, propanol and propionic acid concentrations (Lilly, et al., FEMS Yeast Res. 6(5):726-743, 2006). Overexpression of Bat2p has been reported to result in increases in isobutanol concentrations (Lilly, et al., supra; Chen, et al., Biotechnology for Biofuels 4:21, 2011); similarly, overexpression of Bat1p has been reported to result in increases in isoamyl alcohol concentrations (Yoshimoto, et al., Appl, Microbiol. Biotechnol. 59:501-508, 2002; Lilly et al., supra).

The recombinant yeast of the present invention comprises at least one modification to an Ehrlich pathway gene, thereby changing the expression or activity of a polypeptide encoded by the Erhlich pathway genes by deleting, mutating, substituting, up-regulating, down-regulating, altering the cellular location, altering the state of the protein, and/or adding a cofactor.

Thus, in one embodiment, the recombinant yeast of the present invention comprises at least one upregulated Ehrlich pathway gene, wherein said upregulation increases the rate and/or yield of fusel alcohol production. For example, since BAT1 and BAT2 are capable of catalyzing conversion of the branched chain amino acids to their α-keto acid counterparts (i.e., L-isoleucine→2-keto-3-methyl-valerate, L-leucine→α-ketoisocaproate and L-valine→2-keto-isovalerate, respectively), it is expected that upregulation of either of these transaminases (or both in combination) will lead to increased flux through the Ehrlich pathway resulting in an increased concentration of fusel alcohol from these amino acids. When performed in combination with processing methods to increase the availability of these branched chain amino acids in the fermentation medium, this may increase the overall butanol and fusel alcohol yield per unit of biomass. If the recombinant yeast is engineered to function as an isobutanologen, isobutanol is produced through the isobutanol biosynthetic pathway introduced into the yeast and as a result of increased conversion of valine to isobutanol through the Ehrlich pathway when BAT2 is upregulated, thereby resulting in increased product yield.

Similarly, since ARO8 and ARO9 are capable of catalyzing conversion of the aromatic amino acids to their α-keto acid counterparts (i.e., L-tyrosine→p-hydroxyphenylpyruvate, L-phenylalanine→phenylpyruvate, L-tryptophan→indolepyruvate, respectively), it is expected that upregulation of either of these aromatic aminotransferase will lead to increased flux through the Ehrlich pathway resulting in an increased concentration of fusel alcohol from these amino acids.

In another embodiment, the recombinant yeast of the present invention may comprise at least one down-regulated Ehrlich pathway gene, thereby minimizing the rate and/or yield of fusel alcohol production. This may be advantageous if it is desirable to increase the purity of the primary product of the butanol biosynthetic pathway (i.e., 1-butanol, 2-butanol, isobutanol) and minimize co-production of fusel alcohol, primarily non-isobutanol fusel alcohol. Thus, one of skill in the art will be able to envision means to partially or completely down-regulate the activity of at least one of the Ehrlich pathway enzymes, by creating an insertion, deletion, or targeted mutation within a portion of e.g., BAT1, BAT2, ARO8, ARO9, ARO10, that results in e.g., a complete gene knockout such that the gene is deleted from the genome and no protein is translated.

In an alternate embodiment, expression of one or more of the transaminases BAT1 or BAT2 is up-regulated while expression of the transaminases ARO8 or ARO9 are reduced or eliminated. Gene deletion cassettes causing reduced or eliminated expression are well-known in the art, and are available for purchase from ATCC (i.e., aro8D; ATCC No. 4004569).

Butanol Biosynthetic Pathways

TABLE 3 Summary Of Substrate to Product Conversions In An Example 1-Butanol Biosynthetic Pathway Enzyme [Example E.C. number associated with substrate to product Reaction Substrate To Product Conversion conversion] A acetyl-CoA → acetoacetyl-CoA acetyl-CoA acetyltransferase [E.C. 2.3.1.9] b acetoacetyl-CoA → 3-hydroxybutyryl- 3-hydroxybutyryl-CoA dehydrogenase CoA [E.C. 1.1.1.35, E.C. 1.1.1.30, E.C. 1.1.1.157 and E.C. 1.1.1.36] c 3-hydroxybutyryl-CoA → crotonyl-CoA Crotonase [E.C. 4.2.1.17 and E.C. 4.2.1.55] d crotonyl-CoA → butyryl-CoA butyryl-CoA dehydrogenase [E.C. 1.3.1.44 and E.C. 1.3.1.38] e butyryl-CoA → butyraldehyde butyraldehyde dehydrogenase [E.C. 1.2.1.57] f butyraldehyde → 1-butanol 1-butanol dehydrogenase Note: Suitable polypeptide sequences that encode enzymes which catalyze the substrate to product conversions of the pathway as well as E.C. numbers corresponding to substrate to product conversions for the indicated pathway steps include, but are not limited to, those set forth above. Suitable enzymes associated with the given E.C. numbers will be readily available to those of skill in the art, for example, through online public databases such as the BRENDA database (www.brenda-enzymes.org/) and in the art (for example, in U.S. Patent Application Publication No. 2008/0182308A1, incorporated herein by reference).

TABLE 4 Summary Of Substrate to Product Conversions In Example 2-Butanol Biosynthetic Pathways Pathway III Substrate To Product Conversion [Example E.C. number Pathway I associated with Substrate To substrate to Product product Reaction Conversion Enzyme conversion] Enzyme A pyruvate → acetolactate pyruvate → acetolactate synthase alpha- synthase alpha- EC 2.2.1.6 acetolactate EC 2.2.1.6 acetolactate B alpha- acetolactate alpha- acetolactate acetolactate → decarboxylase acetolactate → decarboxylase [EC acetoin [EC 4.1.1.5] acetoin 4.1.1.5] C acetoin → 3- acetoin aminase — — amino-2- butanol D 3-amino-2- aminobutanol — — butanol → 3- kinase amino-2- butanol O- phosphate E 3-amino-2- aminobutanol — — butanol phosphate phosphate → 2- phospho-lyase butanone I — — acetoin → 2,3- butanediol butanediol dehydrogenase J — — 2,3-butanediol butanediol → 2-butanone dehydratase [EC 4.2.1.28 and EC 4.2.1.30] F 2-butanone → butanol 2-butanone → 2- butanol 2-butanol dehydrogenase butanol dehydrogenase Note: Suitable polypeptide sequences that encode enzymes which catalyze the substrate to product conversions of the pathway as well as E.C. numbers corresponding to substrate to product conversions for indicated pathway steps include, but are not limited to, those set forth above. Suitable enzymes capable of catalyzing the substrate to product conversions associated with the given E.C. numbers will be readily available to those of skill in the art, for example, through public databases such as the BRENDA database (www.brenda-enzymes.org/) and in the art (for example, in U.S. Pat. No. 8,206,970 and U.S. Patent Application Publication No. 2007/0292927A1, each incorporated herein by reference).

TABLE 5 Summary Of Substrate to Product Conversions In Example Isobutanol Biosynthetic Pathways Pathway II Enzyme [Example Pathway I E.C. number Pathway III Substrate To Substrate To associated with Substrate To Product Product substrate to product Product Reaction Conversion Enzyme Conversion conversion] Conversion Enzyme A pyruvate → acetolactate pyruvate → acetolactate pyruvate → acetolactate acetolactate synthase acetolactate synthase acetolactate synthase [EC 2.2.1.6] [EC 2.2.1.6] [EC 2.2.1.6] B acetolactate → acetohydroxy acetolactate → acetohydroxy acid acetolactate → acetohydroxy 2,3-dihydroxy- acid isomer- 2,3-dihydroxy- isomer-reductase 2,3-dihydroxy- acid isomer- isovalerate reductase isovalerate [EC 1.1.1.86] isovalerate reductase [EC 1.1.1.86] [EC 1.1.1.86] C 2,3-dihydroxy- acetohydroxy 2,3-dihydroxy- acetohydroxy acid 2,3-dihydroxy- acetohydroxy isovalerate → α- acid isovalerate → α- dehydratase isovalerate → α- acid ketoisovalerate dehydratase ketoisovalerate [EC 4.2.1.9] ketoisovalerate dehydratase [EC 4.2.1.9] [EC 4.2.1.9] D α-ketoisovalerate branched-chain — — — — → keto acid isobutyraldehyde decarboxylase [EC 4.1.1.72 or EC 4.1.1.1] F — — α-ketoisovalerate branched-chain — — → isobutyryl- keto acid CoA dehydrogenase G — — isobutyryl-CoA acylating aldehyde — — → dehydrogenase isobutyraldehyde H — — — — α-ketoisovalerate valine → valine dehydrogenase or transaminase I — — — — valine to valine isobutylamine decarboxylase J — — — — isobutylamine to omega isobutyraldehyde transaminase E isobutyraldehyde branched- isobutyraldehyde branched- isobutyraldehyde branched- → isobutanol chain alcohol → isobutanol chain alcohol → isobutanol chain alcohol dehydrogenase dehydrogenase dehydrogenase [EC 1.1.1.265, [EC 1.1.1.265, [EC 1.1.1.265, EC 1.1.1.1 or EC 1.1.1.1 or EC 1.1.1.1 or EC 1.1.1.2] EC 1.1.1.2] EC 1.1.1.2] Note: Suitable polypeptide sequences that encode enzymes which catalyze the substrate to product conversions of the pathway as well as E.C. numbers corresponding to substrate to product conversions for indicated pathway steps include, but are not limited to, those set forth above. Suitable enzymes capable of catalyzing the substrate to product conversions associated with the given E.C. numbers will be readily available to those of skill in the art, for example, through online public databases such as the BRENDA database (http://www.brenda-enzymes.org/), and in the art (for example in U.S. Pat. Nos. 7,851,188; 7,993,889; and 8,178,328, each incorporated herein by reference).

In one embodiment, the invention produces butanol from recently-living plant derived carbon sources, avoiding the negative environmental impact associated with the standard petrochemical processes for butanol production. In one embodiment, the invention provides a method for the production of butanol using recombinant industrial host cells comprising an engineered butanol biosynthetic pathway.

In some embodiments, the butanol biosynthetic pathway comprises at least one polynucleotide, at least two polynucleotides, at least three polynucleotides, at least four polynucleotides, etc. that is/are heterologous to the host cell. In some embodiments, each substrate to product conversion of a butanol biosynthetic pathway in a recombinant host cell is catalyzed by a heterologous polypeptide. In embodiments, the polypeptide catalyzing the substrate to product conversions of acetolactate to 2,3-dihydroxyisovalerate and/or the polypeptide catalyzing the substrate to product conversion of isobutyraldehyde to isobutanol are capable of utilizing NADH as a cofactor.

In some embodiments, the engineered butanol pathway of the butanologen comprises at least one polypeptide selected from the group of enzymes having the following Enzyme Commission Numbers: EC 2.2.1.6, EC 1.1.1.86, EC 4.2.1.9, EC 4.1.1.72, EC 1.1.1.1, EC 1.1.1.265, EC 1.1.1.2, EC 1.2.4.4, EC 1.3.99.2, EC 1.2.1.10, EC 2.3.1.9, EC 2.3.1.16, EC 1.1.1.35, EC 1.1.1.157, EC 1.1.1.36, EC 4.2.1.17, EC 4.2.1.55, EC 1.3.1.44, EC 1.3.1.38, EC 4.1.1.8, EC 4.2.1.28, EC 4.2.1.30, and EC 1.2.1.57.

In some embodiments, the engineered butanol pathway of the butanologen comprises at least one polypeptide selected from the following group of enzymes: acetolactate synthase, acetohydroxy acid isomeroreductase, acetohydroxy acid dehydratase, branched-chain alpha-keto acid decarboxylase, branched-chain alcohol dehydrogenase, acylating aldehyde dehydrogenase, branched-chain keto acid dehydrogenase, butyryl-CoA dehydrogenase, butyraldehyde dehydrogenase, acetyl-CoA acetyltransferase, 3-hydroxybutyryl-CoA dehydrogenase, crotonase, butanol dehydrogenase, acetolactate decarboxylase, acetoin aminase, aminobutanol kinase, aminobutanol phosphate phospho-lyase, dihydroxyacetone kinase, serinol phosphate aminotransferase, butanediol dehydrogenase, diol dehydratase and glycerol dehydratase.

The terms “acetohydroxyacid synthase,” “acetolactate synthase” and “acetolactate synthetase” (abbreviated “ALS”) are used interchangeably herein to refer to a polypeptide(s) having an enzyme activity that catalyzes the conversion of two molecules of pyruvic acid to one molecule of alpha-acetolactate. Example acetolactate synthases are known by the EC number 2.2.1.6 [formerly EC 4.1.3.18] (Enzyme Nomenclature 1992, Academic Press, San Diego, Calif.). Acetolactate synthase may utilize the cofactor thiamin pyrophosphate. These unmodified enzymes are available from a number of sources, including, but not limited to, Bacillus subtilis (GenBank Nos: CAB15618 and Z99122, NCBI (National Center for Biotechnology Information) amino acid sequence, NCBI nucleotide sequence, respectively), Klebsiella pneumoniae (GenBank Nos: AAA25079 and M73842), and Lactococcus lactis (GenBank Nos: AAA25161 and L16975). A suitable B. subtilis acetolactate synthase is set forth herein as SEQ ID NO:135.

The terms “ketol-acid reductoisomerase” (“KARI”), “acetohydroxy acid isomeroreductase” and “acetohydroxy acid reductoisomerase” will be used interchangeably and refer to any polypeptide having a biological function of a ketol-acid reductoisomerase. Such polypeptides include a polypeptide capable of catalyzing the reaction of (S)-acetolactate to 2,3-dihydroxyisovalerate. Example KARI enzymes may be classified as EC number 1.1.1.86 and are available from a vast array of microorganisms, including, but not limited to, Escherichia coli (SEQ ID NO:136) (GenBank Nos: NP_418222 and NC_000913), Saccharomyces cerevisiae (GenBank Nos: NP_013459 and NC_001144), Methanococcus maripaludis (GenBank Nos: CAF30210 and BX957220), Pseudomonas fluorescens (SEQ ID NO:137) and Bacillus subtilis (GenBank Nos: CAB14789 and Z99118). KARIs include Anaerostipes caccae KARI variants “K9G9” and “K9D3” and variants thereof. Ketol-acid reductoisomerase (KARI) enzymes are described in U.S. Pat. Nos. 7,910,342, and 8,129,162; U.S. Patent Application Publication No. 2010/0197519; and International Publication No. WO 2011/041415, all of which are incorporated herein by reference. Examples of KARIs disclosed therein are those from Lactococcus lactis, Vibrio cholera, Pseudomonas aeruginosa PAO1, and Pseudomonas fluorescens PF5 mutants. U.S. Appl. Pub. No. US20130071898A1, incorporated herein by reference, further describes KARI variants useful in the present invention, and is incorporated herein by reference. An example A. caccae KARI (i.e., variant “K9SB2”) is set forth herein as SEQ ID NO:124.

The terms “acetohydroxy acid dehydratase” and “dihydroxyacid dehydratase” (“DHAD”) refer to any polypeptide having a biological function of a dihydroxyacid dehydratase. Such polypeptides include a polypeptide that catalyzes the conversion of 2,3-dihydroxyisovalerate to α-ketoisovalerate. Example acetohydroxy acid dehydratases are known by the EC number 4.2.1.9. Such enzymes are available from a vast array of microorganisms, including, but not limited to, E. coli (GenBank Nos: YP_026248 and NC_000913), S. cerevisiae (GenBank Nos: NP_012550 and NC_001142), M. maripaludis (GenBank Nos: CAF29874 and BX957219), B. subtilis (GenBank Nos:CAB14105 and Z99115), Lactococcus lactis (SEQ ID NO:131), Streptococcus mutans (SEQ ID NO:X126) and N. crassa. U.S. Patent Application Publication No. 2010/0081154 A1 and U.S. Pat. No. 7,993,889, both of which are incorporated herein by reference, describe dihydroxyacid dehydratases (DHADs), including a DHAD from Streptococcus mutans and a DHAD from Lactococcus lactis. The term “branched-chain α-keto acid decarboxylase” or “α-ketoacid decarboxylase” or “α-ketoisovalerate decarboxylase” or “2-ketoisovalerate decarboxylase” (“KIVD”) refers to any polypeptide having a biological function of a 2-ketoisovalerate decarboxylase. Such polypeptides include a polypeptide that catalyzes the conversion of α-ketoisovalerate to isobutyraldehyde and CO₂. Example branched chain α-keto acid decarboxylases are known by the EC number 4.1.1.72 and are available from a number of sources, including, but not limited to, Lactococcus lactis (GenBank Nos: AAS49166, AY548760, CAG34226 and AJ746364), Salmonella typhimurium (GenBank Nos: NP_461346 and NC_003197), Clostridium acetobutylicum (GenBank Nos: NP_149189 and NC_001988), Macrococcus caseolyticus (SEQ ID NO:133), and Listeria grayi (SEQ ID NO:128).

The terms “branched-chain alcohol dehydrogenase” or “alcohol dehydrogenase” (“ADH”) refer to any polypeptide having a biological function of an alcohol dehydrogenase. Such polypeptides include a polypeptide that catalyzes the conversion of isobutyraldehyde to isobutanol. Example branched-chain alcohol dehydrogenases are known by the EC number 1.1.1.265, but may also be classified under other alcohol dehydrogenases (specifically, EC 1.1.1.1 or 1.1.1.2). Such enzymes are available from a number of sources, including, but not limited to, S. cerevisiae (GenBank Nos: NP_010656, NC_001136, NP_014051 and NC_001145), E. coli (GenBank Nos: NP_417484 and NC_000913), C. acetobutylicum (GenBank Nos: NP_349892, NC_003030, NP_349891 and NC_003030), Beijerinckia indica (SEQ ID NO:129) and Achromobacter xylosoxidans (SEQ ID NO:134). U.S. Pat. No. 8,188,250, incorporated herein by reference, describes SadB, an alcohol dehydrogenase (ADH) from A. xylosoxidans. Alcohol dehydrogenases also include horse liver ADH and B. indica ADH (as described by U.S. Patent Application Publication No. 20110269199, incorporated herein by reference).

The term “butanol dehydrogenase” refers to any polypeptide having a biological function of a butanol dehydrogenase. Such polypeptides include a polypeptide that catalyzes the conversion of isobutyraldehyde to isobutanol or the conversion of 2-butanone to 2-butanol. Butanol dehydrogenases are a subset of a broad family of alcohol dehydrogenases. Example enzymes are known as EC 1.1.1.1 and are available, for example, from Rhodococcus ruber (GenBank Nos: CAD36475 and AJ491307). Other example enzymes are known as EC 1.1.1.2 and are available, for example, from Pyrococcus furiosus (GenBank Nos: AAC25556 and AF013169). Additionally, a butanol dehydrogenase is available from Escherichia coli (GenBank Nos: NP_417484 and NC_000913) and a cyclohexanol dehydrogenase is available from Acinetobacter sp. (GenBank Nos: AAG10026 and AF282240). The term “butanol dehydrogenase” also refers to an enzyme that catalyzes the conversion of butyraldehyde to 1-butanol, using either NADH or NADPH as cofactor. Butanol dehydrogenases are available from, for example, C. acetobutylicum (GenBank Nos: NP_149325 and NC_001988 (note: this enzyme possesses both aldehyde and alcohol dehydrogenase activity), NP_349891, NC_003030, NP_349892 and NC_003030) and E. coli (GenBank Nos: NP_417484 and NC_000913).

The term “branched-chain keto acid dehydrogenase” refers to any polypeptide having a biological function of a branched-chain keto acid dehydrogenase. Such polypeptides include a polypeptide that catalyzes the conversion of α-ketoisovalerate to isobutyryl-CoA (isobutyryl-coenzyme A), typically using NAD₊ (nicotinamide adenine dinucleotide) as an electron acceptor. Example branched-chain keto acid dehydrogenases are known by the EC number 1.2.4.4. Such branched-chain keto acid dehydrogenases are comprised of four subunits and sequences from all subunits are available from a vast array of microorganisms, including, but not limited to, B. subtilis (GenBank Nos: CAB14336, Z99116, CAB14335, Z99116, CAB14334, Z99116, CAB14337 and Z99116) and Pseudomonas putida (GenBank Nos: AAA65614, M57613, AAA65615, M57613, AAA65617, M57613, AAA65618 and M57613).

The term “acylating aldehyde dehydrogenase” refers to any polypeptide having a biological function of an acylating aldehyde dehydrogenase. Such polypeptides include a polypeptide that catalyzes the conversion of isobutyryl-CoA to isobutyraldehyde, typically using either NADH or NADPH as an electron donor. Example acylating aldehyde dehydrogenases are known by the EC numbers 1.2.1.10 and 1.2.1.57. Such enzymes are available from multiple sources, including, but not limited to, Clostridium beijerinckii (GenBank Nos: AAD31841 and AF157306), C. acetobutylicum (GenBank Nos: NP_149325, NC_001988, NP_149199 and NC_001988), P. putida (GenBank Nos: AAA89106 and U13232), and Thermus thermophilus (GenBank Nos: YP_145486 and NC_006461).

The term “acetyl-CoA acetyltransferase” refers to any polypeptide having a biological function of an acetyl-CoA acetyltransferase. Such polypeptides include a polypeptide that catalyzes the conversion of two molecules of acetyl-CoA to acetoacetyl-CoA and coenzyme A (CoA). Example acetyl-CoA acetyltransferases are acetyl-CoA acetyltransferases with substrate preferences (reaction in the forward direction) for a short chain acyl-CoA and acetyl-CoA and are classified as E.C. 2.3.1.9; although, enzymes with a broader substrate range (E.C. 2.3.1.16) will be functional as well. Acetyl-CoA acetyltransferases are available from a number of sources, for example, Escherichia coli (GenBank Nos: NP_416728 and NC_000913), Clostridium acetobutylicum (GenBank Nos: NP_349476.1, NC_003030, NP_149242 and NC_001988, Bacillus subtilis (GenBank Nos: NP_390297 and NC_000964), and Saccharomyces cerevisiae (GenBank Nos: NP_015297 and NC_001148).

The term “3-hydroxybutyryl-CoA dehydrogenase” refers to any polypeptide having a biological function of a 3-hydroxybutyryl-CoA dehydrogenase. Such polypeptides include a polypeptide that catalyzes the conversion of acetoacetyl-CoA to 3-hydroxybutyryl-CoA. Example 3-hydroxybutyryl-CoA dehydrogenases may be reduced nicotinamide adenine dinucleotide (NADH)-dependent, with a substrate preference for (S)-3-hydroxybutyryl-CoA or (R)-3-hydroxybutyryl-CoA. Examples may be classified as E.C. 1.1.1.35 and E.C. 1.1.1.30, respectively. Additionally, 3-hydroxybutyryl-CoA dehydrogenases may be reduced nicotinamide adenine dinucleotide phosphate (NADPH)-dependent, with a substrate preference for (S)-3-hydroxybutyryl-CoA or (R)-3-hydroxybutyryl-CoA and are classified as E.C. 1.1.1.157 and E.C. 1.1.1.36, respectively. 3-Hydroxybutyryl-CoA dehydrogenases are available from a number of sources, for example, C. acetobutylicum (GenBank Nos: NP_349314 and NC_003030), B. subtilis (GenBank Nos: AAB09614 and U29084), Ralstonia eutropha (GenBank Nos:YP_294481 and NC_007347), and Alcaligenes eutrophus (GenBank Nos: AAA21973 and J04987).

The term “crotonase” refers to any polypeptide having a biological function of a crotonase. Such polypeptides include a polypeptide that catalyzes the conversion of 3-hydroxybutyryl-CoA to crotonyl-CoA and H2O. Example crotonases may have a substrate preference for (S)-3-hydroxybutyryl-CoA or (R)-3-hydroxybutyryl-CoA and may be classified as E.C. 4.2.1.17 and E.C. 4.2.1.55, respectively. Crotonases are available from a number of sources, for example, E. coli (GenBank Nos: NP_415911 and NC_000913), C. acetobutylicum (GenBank Nos: NP_349318 and NC_003030), B. subtilis (GenBank Nos: CAB13705 and Z99113), and Aeromonas caviae (GenBank Nos:BAA21816 and D88825).

The term “butyryl-CoA dehydrogenase” refers to any polypeptide having a biological function of a butyryl-CoA dehydrogenase. Such polypeptides include a polypeptide that catalyzes the conversion of crotonyl-CoA to butyryl-CoA. Example butyryl-CoA dehydrogenases may be NADH-dependent, NADPH-dependent, or flavin dependent and may be classified as E.C. 1.3.1.44, E.C. 1.3.1.38, and E.C. 1.3.99.2, respectively. Butyryl-CoA dehydrogenases are available from a number of sources, for example, C. acetobutylicum (GenBank Nos: NP_347102 and NC_003030), Euglena gracilis (GenBank Nos: Q5EU90 and AY741582), Streptomyces collinus (GenBank Nos:AAA92890 and U37135), and Streptomyces coelicolor (GenBank Nos: CAA22721 and AL939127).

The term “butyraldehyde dehydrogenase” refers to any polypeptide having a biological function of a butyraldehyde dehydrogenase. Such polypeptides include a polypeptide that catalyzes the conversion of butyryl-CoA to butyraldehyde, using NADH or NADPH as cofactor. Butyraldehyde dehydrogenases with a preference for NADH are known as E.C. 1.2.1.57 and are available from, for example, Clostridium beijerinckii (GenBank Nos: AAD31841 and AF157306) and C. acetobutylicum (GenBank Nos:NP_149325 and NC_001988).

The term “transaminase” refers to an enzyme that catalyzes the conversion of α-ketoisovalerate to L-valine, using either alanine or glutamate as amine donor. Example transaminases are known by the EC numbers 2.6.1.42 and 2.6.1.66. These enzymes are available from a number of sources. Examples of sources for alanine-dependent enzymes include, but are not limited to, E. coli (GenBank Nos: YP_026231, NC_000913) and Bacillus licheniformis (GenBank Nos: YP_093743, NC_006322). Examples of sources for glutamate-dependent enzymes include, but are not limited to, E. coli (GenBank Nos: YP_026247, NC_000913), S. cerevisiae (GenBank Nos: NP_012682, NC_001142) and Methanobacterium thermoautotrophicum (GenBank Nos: NP_276546, NC_000916).

The term “valine dehydrogenase” refers to an enzyme that catalyzes the conversion of α-ketoisovalerate to L-valine, using NAD(P)H as electron donor and ammonia as amine donor. Example valine dehydrogenases are known by the EC numbers 1.4.1.8 and 1.4.1.9 and are available from a number of sources, including, but not limited to, Streptomyces coelicolor (GenBank Nos: NP_628270, NC_003888) and B. subtilis (GenBank Nos: CAB14339, Z99116).

The term “valine decarboxylase” refers to an enzyme that catalyzes the conversion of L-valine to isobutylamine and CO₂. Example valine decarboxylases are known by the EC number 4.1.1.14. These enzymes are found in Streptomycetes, such as for example, Streptomyces viridifaciens (GenBank Nos: AAN10242, AY116644).

The term “omega transaminase” refers to an enzyme that catalyzes the conversion of isobutylamine to isobutyraldehyde using a suitable amino acid as amine donor. Example omega transaminases are known by the EC number 2.6.1.18 and are available from a number of sources, including, but not limited to, Alcaligenes denitrificans (AAP92672, AY330220), Ralstonia eutropha (GenBank Nos: YP_294474, NC_007347), Shewanella oneidensis (GenBank Nos: NP_719046, NC_004347), and P. putida (GenBank Nos: AAN66223, AE016776).

The term “isobutyryl-CoA mutase” refers to an enzyme that catalyzes the conversion of butyryl-CoA to isobutyryl-CoA. This enzyme uses coenzyme B₁₂ as cofactor. Example isobutyryl-CoA mutases are known by the EC number 5.4.99.13. These enzymes are found in a number of Streptomycetes.

The term “acetolactate decarboxylase” refers to a polypeptide (or polypeptides) having an enzyme activity that catalyzes the conversion of alpha-acetolactate to acetoin. Acetolactate decarboxylases are known as EC 4.1.1.5 and are available, for example, from Bacillus subtilis [GenBank Nos: AAA22223, L04470], Klebsiella terrigena [GenBank Nos: AAA25054, L04507], and Klebsiella pneumoniae [GenBank Nos: AAU43774, AY722056].

The term “acetoin aminase” or “acetoin transaminase” refers to a polypeptide (or polypeptides) having an enzyme activity that catalyzes the conversion of acetoin to 3-amino-2-butanol. An example acetoin aminase, also known as amino alcohol dehydrogenase, is described by Ito, et al. (U.S. Pat. No. 6,432,688). Another example is the amine:pyruvate aminotransferase (also called amine:pyruvate transaminase) described by Shin and Kim (J. Org. Chem. 67:2848-2853, 2002).

The term “aminobutanol phosphate phospho-lyase,” also called “amino alcohol O-phosphate lyase,” refers to a polypeptide (or polypeptides) having an enzyme activity that catalyzes the conversion of 3-amino-2-butanol O-phosphate to 2-butanone. U.S. Patent Application Publication No. 2007/0259410 describes an aminobutanol phosphate phospho-lyase from the Erwinia carotovora subsp. atroseptica.

The term “aminobutanol kinase” refers to a polypeptide (or polypeptides) having an enzyme activity that catalyzes the conversion of 3-amino-2-butanol to 3-amino-2-butanol O-phosphate. Aminobutanol kinase may utilize ATP as the phosphate donor. U.S. Patent Application Publication No. 2007/0259410 describes an amino alcohol kinase of Erwinia carotovora subsp. atroseptica.

The term “butanediol dehydrogenase” also known as “acetoin reductase” refers to a polypeptide (or polypeptides) having an enzyme activity that catalyzes the conversion of acetoin to 2,3-butanediol. Butanediol dehydrogenases are a subset of the broad family of alcohol dehydrogenases. Butanediol dehydrogenase enzymes may have specificity for production of (R)- or (S)-stereochemistry in the alcohol product. Example (S)-specific butanediol dehydrogenases are known as EC 1.1.1.76 and are available, for example, from Klebsiella pneumoniae (GenBank Nos: BBA13085, D86412). Example (R)-specific butanediol dehydrogenases are known as EC 1.1.1.4 and are available, for example, from Bacillus cereus [GenBank Nos. NP_830481, NC_004722, AAP07682, AE017000], and Lactococcus lactis [GenBank Nos. AAK04995, AE006323].

The term “butanediol dehydratase,” also known as “diol dehydratase” or “propanediol dehydratase” refers to a polypeptide (or polypeptides) having an enzyme activity that catalyzes the conversion of 2,3-butanediol to 2-butanone. Butanediol dehydratase may utilize the cofactor adenosyl cobalamin (vitamin B12). Adenosyl cobalamin-dependent enzymes are known as EC 4.2.1.28 and are available, for example, from Klebsiella oxytoca [GenBank Nos: BAA08099 (alpha subunit), D45071; BAA08100 (beta subunit), D45071; and BBA08101 (gamma subunit), D45071 (Note all three subunits are required for activity)], and Klebsiella pneumoniae [GenBank Nos: AAC98384 (alpha subunit), AF102064; GenBank Nos: AAC98385 (beta subunit), AF102064, GenBank Nos: AAC98386 (gamma subunit), AF102064]. Other suitable diol dehydratases include, but are not limited to, B12-dependent diol dehydratases available from Salmonella typhimurium [GenBank Nos: AAB84102 (large subunit), AF026270; GenBank Nos: AAB84103 (medium subunit), AF026270; GenBank Nos: AAB84104 (small subunit), AF026270]; and Lactobacillus collinoides [GenBank Nos: CAC82541 (large subunit), AJ297723; GenBank Nos: CAC82542 (medium subunit); AJ297723; GenBank Nos: CAD01091 (small subunit), AJ297723]; and enzymes from Lactobacillus brevis (particularly strains CNRZ 734 and CNRZ 735, Speranza, et al., supra), and nucleotide sequences that encode the corresponding enzymes. Methods of diol dehydratase gene isolation are well known in the art (e.g., U.S. Pat. No. 5,686,276).

The term “glycerol dehydratase” refers to a polypeptide (or polypeptides) having an enzyme activity that catalyzes the conversion of glycerol to 3-hydroxypropionaldehyde. Adenosyl cobalamin-dependent glycerol dehydratases are known as EC 4.2.1.30. The glycerol dehydratases of EC 4.2.1.30 are similar to the diol dehydratases in sequence and in having three subunits. The glycerol dehydratases can also be used to convert 2,3-butanediol to 2-butanone. Some examples of glycerol dehydratases of EC 4.2.1.30 include those from Klebsiella pneumoniae; from Clostridium pasteurianum [GenBank Nos: 3360389 (alpha subunit), 3360390 (beta subunit), and 3360391 (gamma subunit)]; from Escherichia blattae [GenBank Nos: 60099613 (alpha subunit), 57340191 (beta subunit), and 57340192 (gamma subunit)]; and from Citrobacter freundii [GenBank Nos: 1169287 (alpha subunit), 1229154 (beta subunit), and 1229155 (gamma subunit)]. Note that all three subunits are required for activity.

Methods for Producing a Recombinant Yeast Containing an Engineered Isobutanol Biosynthetic Pathway Containing a Modified Biosynthetic Production Matrix

In embodiments, the recombinant yeast containing an engineered isobutanol biosynthetic pathway contains a biosynthetic production matrix for the production of isobutanol and other fusel alcohols. The biosynthetic production matrix contains various branch points where the production of one or more fusel alcohols can be modulated. This modulation can occur through genetic modification of the yeast chromosome so that specific genes or regulatory elements involved in the fusel alcohol production pathways are altered.

For example, in one embodiment, the recombinant yeast with engineered isobutanol biosynthetic pathway contains genomic modifications resulting in reduced or eliminated 1-propanol, 2-methyl-1-butanol, and 3-methyl-1-butanol production, and enhanced production of isobutanol. One non-limiting example of such a recombinant yeast is a yeast cell comprising a complete or partial deletion of the LEU4, LEU9, and ILV1 genes (optionally BAT1 and BAT2). Reduced or eliminated expression of the LEU4, LEU9, and ILV1 genes can be achieved by methods known in the art, such as deletions, frameshift mutations, point mutations which disrupt enzyme activity/structure, or modification of regulatory elements (e.g., promoters) that reduce or eliminate expression.

For example, in one embodiment, the recombinant yeast with engineered isobutanol biosynthetic pathway contains genomic modifications resulting in enhanced 1-propanol, 2-methyl-1-butanol, 3-methyl-1-butanol, and isobutanol production. One non-limiting example of such a recombinant yeast is a yeast cell comprising upregulation of the LEU4, LEU9, ILV1, BAT1, and BAT2 genes. Upregulation of these genes, for example LEU4, can be achieved by methods known in the art, such as by promoter replacement with a strong promoter (for example, FBA1), or by introducing multiple copies of the LEU4 gene into the chromosome.

In another embodiment, the recombinant yeast with engineered isobutanol biosynthetic pathway contains genomic modifications resulting in reduced or eliminated 1-propanol and 2-methyl-1-butanol production, but enhanced production of isobutanol and 3-methyl-1-butanol production. One non-limiting example of such a recombinant yeast is a yeast cell comprising upregulation of the LEU4 and LEU9 genes (optionally BAT1 and BAT2) and a complete or partial deletion of the ILV1 gene. Upregulation of these genes, for example LEU4, can be achieved by methods known in the art, such as by promoter replacement with a strong promoter (for example, FBA1), or by introducing multiple copies of the LEU4 gene into the chromosome. Reduced or eliminated expression of the ILV1 gene can be achieved by methods known in the art, such as deletions, frameshift mutations, point mutations which disrupt enzyme activity/structure, or modification of regulatory elements (e.g., promoters) that reduce or eliminate expression.

Yeast Host Cells for Butanol Production

Host cells for butanol production in the present invention comprise yeast. In general, suitable host cells include any yeast cell useful for genetic modification and recombinant gene expression. The criteria for selection of suitable microbial hosts include the following: intrinsic tolerance to the butanol isomer being produced, high rate of glucose utilization, availability of genetic tools for gene manipulation, and the ability to generate stable chromosomal alterations.

The ability to genetically modify the host is a consideration for the production of any recombinant microorganism. The mode of gene transfer technology may be by electroporation, conjugation, transduction or natural transformation. A broad range of host conjugative plasmids and drug resistance markers are available. The cloning vectors are tailored to the host organisms based on the nature of antibiotic resistance markers that can function in that host.

The microbial host also has to be manipulated in order to inactivate competing pathways for carbon flow by deleting various genes. This requires the availability of either transposons to direct inactivation or chromosomal integration vectors. Additionally, the production host should be amenable to chemical mutagenesis so that mutations to improve intrinsic butanol tolerance may be obtained.

The microbial host cell used for the production butanol isomers is preferably tolerant to the butanol isomer that is being produced so that the yield of the butanol isomer is not limited by the toxicity of the butanol isomer. In one embodiment, the host used for the isobutanol production is tolerant to isobutanol. Suitable host strains with a tolerance for isobutanol may be identified by a screening method based on the intrinsic tolerance of the strain as described in U.S. Pat. No. 7,993,889 (incorporated herein by reference).

The microbial host for isobutanol production should also utilize carbohydrates including monosaccharides, oligosaccharides and polysaccharides, at a high rate. Most microbes are capable of utilizing carbohydrates. However, certain environmental microbes cannot utilize carbohydrates to high efficiency, and therefore would not be suitable hosts.

Based on the criteria described above, suitable yeasts for the production of butanol in the present invention include, but are not limited to, crabtree-positive yeast selected from Saccharomyces, Zygosaccharomyces, Schizosaccharomyces, Dekkera, Torulopsis, Brettanomyces, and some species of Candida. Species of crabtree-positive yeast include, but are not limited to, Saccharomyces cerevisiae, Saccharomyces kluyveri, Schizosaccharomyces pombe, Saccharomyces bayanus, Saccharomyces mikatae, Saccharomyces paradoxus, Zygosaccharomyces rouxii, and Candida glabrata.

In some embodiments, the host cell is Saccharomyces cerevisiae. S. cerevisiae yeast are known in the art and are available from a variety of sources including, but not limited to, American Type Culture Collection (Rockville, Md.), Centraalbureau voor Schimmelcultures (CBS) Fungal Biodiversity Centre, LeSaffre, Gert Strand AB, Ferm Solutions, North American Bioproducts, Martrex, and Lallemand. S. cerevisiae include, but are not limited to, BY4741, CEN.PK 113-7D, Ethanol Red® yeast, Ferm Pro™ yeast, Bio-Ferm® XR yeast, Gert Strand Prestige Batch Turbo alcohol yeast, Gert Strand Pot Distillers yeast, Gert Strand Distillers Turbo yeast, FerMax™ Green yeast, FerMax™ Gold yeast, Thermosacc® yeast, BG-1, PE-2, CAT-1, CBS7959, CBS7960, and CBS7961.

Recombinant yeast containing the genes necessary to encode the enzymatic pathway for conversion of a fermentable carbon substrate to butanol isomers may be constructed using techniques well known in the art. In the present invention, genes encoding the enzymes of one of the butanol biosynthetic pathways, for example, acetolactate synthase, acetohydroxy acid isomeroreductase, acetohydroxy acid dehydratase, branched-chain α-keto acid decarboxylase, and branched-chain alcohol dehydrogenase, may be isolated from various sources, as described, for example, herein, and in U.S. Pat. No. 7,993,889 and U.S. Patent Application Publication No. 2013/0071898A1, both incorporated by reference.

Relevant enzymes of the butanol biosynthetic pathway may be introduced into yeast cells, as described, for example, in U.S. Pat. No. 7,993,889, incorporated by reference, to produce butanologens. The butanologens generated comprise an engineered butanol biosynthetic pathway. In some embodiments, the butanologen is an isobutanologen, which comprises an engineered isobutanol biosynthetic pathway. In some embodiments, the butanologen is Saccharomyces cerevisiae.

In some embodiments, enzymes of the butanol biosynthetic pathway are not localized to the mitochondria. In some embodiments, enzymes of the engineered butanol biosynthetic pathway are localized to the cytosol. In some embodiments, an enzyme of the biosynthetic pathway is localized to the cytosol by removing the mitochondrial targeting sequence. In some embodiments, mitochondrial targeting is eliminated by generating new start codons as described in for example, U.S. Pat. No. 7,993,889, incorporated herein by reference. In some embodiments, an enzyme of the biosynthetic pathway that is localized to the cytosol is DHAD. In some embodiments, an enzyme from the biosynthetic pathway that is localized to the cytosol is KARI.

Additional Modifications within Butanologens

The butanologens as provided herein may further comprise one or more additional modifications. Such modifications, for example, may include disruption of the activity of the genes involved in the production of by-products during the fermentative production of butanol isomers via the engineered butanol biosynthetic pathway. The disruption of the activity of the genes involved in the production of by-products during the fermentative production of butanol isomers reduces yield loss from the competing pathways for carbon flow and increases butanol production. In some embodiments, such modifications include disruption of the activity of pyruvate decarboxylase, aldehyde dehydrogenase or both.

The term “pyruvate decarboxylase” refers to any polypeptide having a biological function of a pyruvate decarboxylase. Such polypeptides include a polypeptide that catalyzes the decarboxylation of pyruvic acid to acetaldehyde and CO₂. Pyruvate decarboxylases are known by the EC number 4.1.1.1. Such polypeptides can be determined by methods well known in the art and disclosed in U.S. Patent Application Publication No. 2013/0071898A1, incorporated herein by reference. These enzymes are found in a number of yeast, including Saccharomyces cerevisiae (GenBank Nos: CAA97575, CAA97705 and CAA97091). Additional examples of PDC are provided in U.S. Patent Application Publication No. 2009/035363, which is incorporated herein by reference.

In some embodiments, a butanologen disclosed herein can comprise a modification or disruption of an endogenous polynucleotide and/or gene encoding a polypeptide having pyruvate decarboxylase activity and/or an endogenous polypeptide having pyruvate decarboxylase activity. In some embodiments, a butanologen disclosed herein can comprise a deletion, mutation, and/or substitution in an endogenous polynucleotide or gene encoding a polypeptide having PDC activity, or in an endogenous polypeptide having PDC activity. Such modifications, disruptions, deletions, mutations, and/or substitutions can result in PDC activity that is reduced or eliminated, resulting, for example, in a PDC knock-out (PDC-KO) phenotype.

Endogenous pyruvate decarboxylase in yeast converts pyruvate to acetaldehyde, which is then converted to ethanol or to acetyl-CoA via acetate. Yeast may have one or more genes encoding pyruvate decarboxylase. For example, there is one gene encoding pyruvate decarboxylase in Candida glabrata, Schizosaccharomyces pombe and Kluyveromyces lactis, while there are three isozymes of pyruvate decarboxylase encoded by the PDC1, PCD5 and/or PDC6 genes in Saccharomyces. In some embodiments, in the present yeast cells at least one PDC gene is inactivated. If the yeast cell used has more than one expressed (active) PDC gene, then each of the active PDC genes may be modified or inactivated thereby producing a pdc-cell. For example, in S. cerevisiae the PDC1, PDC5 and PDC6 genes may be modified or inactivated. If a PDC gene is not active under the fermentation conditions to be used then such a gene would not need to be modified or inactivated. In some embodiments, the pyruvate decarboxylase that is deleted or downregulated is selected from the group consisting of: PDC1, PDC5, PDC6 and combinations thereof. U.S. Patent Application Publication No. 2009/0305363 and U.S. Patent Application Publication No. 2013/0071898A1 (both incorporated herein by reference) further describe the modifications in the endogenous pyruvate decarboxylase, and are incorporated herein by reference. U.S. Patent Application Publication No. 2009/0305363 (incorporated herein by reference) discloses increased conversion of pyruvate to acetolactate by engineering yeast for expression of a cytosol-localized acetolactate synthase and substantial elimination of pyruvate decarboxylase activity. Yeast having a reduced enzymatic activity can be identified using various methods. For example, yeast having reduced pyruvate decarboxylase activity can be identified using common methods, including, for example, measuring ethanol formation via gas chromatography.

Other target genes, such as those encoding pyruvate decarboxylase proteins having at least about 70-75%, at least about 75-85%, at least about 80-85%, at least about 85%-90%, at least about 90%-95%, or at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the pyruvate decarboxylases may be identified in the literature and in bioinformatics databases well known to the skilled person. The methods for disruption of pyruvate decarboxylase activity along with the methods for identification of butanologens with modified or deleted pyruvate decarboxylase are described in detail in U.S. Patent Application Publication No. 2009/0305363 and U.S. Patent Application Publication No. 2013/0071898 A1, incorporated herein by reference.

In some embodiments, a butanologen comprises modifications to reduce glycerol-3-phosphate dehydrogenase activity and/or disruption of at least one gene encoding a polypeptide having PDC activity or a disruption in at least one gene encoding a regulatory element controlling PDC gene expression as described in U.S. Patent Application Publication Nos. 2009/0305363 and 2013/0071898A1, both incorporated by reference, the modifications that would provide for an increased carbon flux through Entner-Doudoroff Pathway, or reducing equivalents balance as described in U.S. Patent Application Publication No. 2010/0120105 (incorporated herein by reference). Yeast cells with inactivated endogenous PDC gene and an engineered biosynthethic pathway having improved growth and product yield when glucose repression was reduced are described in U.S. Patent Application Publication No. 2011/0124060, incorporated herein by reference.

The term “aldehyde dehydrogenases” refers to any polypeptide having a biological function of an aldehyde dehydrogenase. Such polypeptides include a polypeptide that catalyzes the oxidation (dehydrogenation) of aldehydes (Wang. et al., J. Bacteriol. 180:822-30, 1998; Navarro-Avino, et al., Yeast 15:829-42, 1999; and Saint-Prix, et al., Microbiology 150:2209-20, 2004). Such polypeptides include a polypeptide that catalyzes the conversion of isobutyraldehyde to isobutyric acid. Such polypeptides also include a polypeptide that corresponds to EC Numbers 1.2.1.3, EC 1.2.1.4 or 1.2.1.5. Such polypeptides can be determined by methods well known in the art and are disclosed in U.S. Patent Application Publication No. 2013/0071898A1, incorporated by reference.

In some embodiments, a butanologen can comprise deletion, mutation and/or substitution in an endogenous polynucleotide or gene encoding a polypeptide having aldehyde dehydrogenase (ALD) and/or aldehyde oxidase activity or deletion, mutation and/or substitution in an endogenous polypeptide having aldehyde dehydrogenase activity and/or aldehyde oxidase activity. In some embodiments, a recombinant host cell of the invention can be S. cerevisiae, and a polypeptide having aldehyde dehydrogenase activity can be ALD2, ALD3, ALD4, ALD5, ALD6, or combinations thereof.

In some embodiments, the polypeptide having aldehyde dehydrogenase activity is ALD6 in Saccharomyces cerevisiae or a homolog thereof. Such modifications, disruptions, deletions, mutations, and/or substitutions can result in ALD activity that is reduced or eliminated, resulting, for example, in an ALD6 knock-out (ALD6-KO) phenotype. Examples of aldehyde dehydrogenase polynucleotides, genes and polypeptides that can be targeted for modification or inactivation in a recombinant host cell are provided in further detail in U.S. Patent Application Publication No. 2013/0071898A1.

The disruption of a particular aldehyde dehydrogenase could be confirmed, for example, with PCR screening using primers internal and external to the aldehyde dehydrogenase gene or by Southern blot using a probe designed to the aldehyde dehydrogenase gene sequence. Alternatively, one could utilize gas chromatography-mass spectroscopy or liquid chromatography to screen strains exposed to isobutyraldehyde for decreased formation of isobutyric acid. For example, a method of screening for strains with decreased isobutyric acid formation can comprise: a) providing a strain comprising a modification in a polynucleotide encoding a polypeptide having aldehyde dehydrogenase activity and/or a modification in a polynucleotide encoding a polypeptide having aldehyde oxidase activity; b) contacting the cell with isobutyraldehyde; and c) measuring isobutyric acid formation; wherein isobutyric acid formation is reduced as compared to a control strain without the modification. In some embodiments, the measuring is carried out using gas chromatography-mass spectroscopy. The methods for deletion, mutation and/or substitution of polynucleotide, gene or polypeptide for aldehyde dehydrogenase and methods for identifying disruption of aldehyde dehydrogenase activity are described in detail, e.g., in U.S. Patent Application Publication No. 2013/0071898A1.

Other target genes, such as those encoding aldehyde dehydrogenase proteins having at least about 70-75%, at least about 75-85%, at least about 80-85%, at least about 85%-90%, at least about 90%-95%, or at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the aldehyde dehydrogenase may be identified in the literature and in bioinformatics databases well known to the skilled person.

In some embodiments, butanologens described herein can comprise a reduced or eliminated aldehyde dehydrogenase and/or aldehyde oxidase activity, as described in U.S. Patent Application Publication No. 2013/0071898 A1. In some embodiments, a butanologen with reduced or eliminated aldehyde dehydrogenase activity can produce a butanol isomer via the engineered biosynthetic pathway at a greater yield or amount than the yield or amount of the same isomer produced by a butanologen that does not comprise reduced or eliminated aldehyde dehydrogenase activity.

In some embodiments, a butanologen as described herein can comprise a deletion, mutation, and/or substitution in an endogenous polynucleotide or gene encoding a polypeptide involved in the pathways for the production of by-products during the fermentative production of butanol isomers. In some embodiments, a butanologen can comprise one or more deletions, mutations, and/or substitutions in an endogenous polypeptide that is involved in the pathways for the production of by-products during the fermentative production of butanol isomers. In some embodiments, butanologens provided herein comprise modifications in genes or polynucleotides encoding URA3 (orotidine-5′-phosphate (OMP) decarboxylase), HIS3 (imidazoleglycerol-phosphate dehydratase), FRA2 (iron repressor protein), CCC1 (putative vacuolar Fe2+/Mn2+ transporter) or GPD2 (glycerol-2-phosphate dehydrogenase) or polypeptides having URA3, HIS3, FRA2, CCC1 or GPD2 activity or combinations thereof as described, for example, in US Patent Application Publication No. 2012/0064561A1, incorporated herein by reference.

In other embodiments, modifications include integration of at least one polynucleotide encoding a polypeptide that catalyzes a step in a pyruvate-utilizing biosynthetic pathway. Other modifications include at least one deletion, mutation, and/or substitution in an endogenous polynucleotide encoding a polypeptide having acetolactate reductase activity. In embodiments, the polypeptide having acetolactate reductase activity is YMR226C of Saccharomyces cerevisiae or a homolog thereof. In other embodiments, a butanologen may comprise modifications including integration of at least one polynucleotide encoding a polypeptide that catalyzes the conversion of xylulose-5-phosphate into glyceraldehyde-3-phosphate and acetyl-phosphate and/or at least one polynucleotide encoding a polypeptide that catalyzes conversion of fructose-6-phosphate into erythrose-4-phosphate and acetyl-phosphate, as described in International Publication No. WO 2011/159853. More specifically, it has been found that expression of enzymes associated with the phosphoketolase pathway (e.g., phosphoketolase [EC 4.1.2.9] and/or phosphotransacetylase [EC 2.3.1.8]) results in a reduced or eliminated requirement for exogenous two-carbon substrate supplementation for growth of PDC-KO cells. Numerous examples of polynucleotides, genes and polypeptides encoding phosphoketolase activity are known in the art and can be used in the recombinant host cells disclosed herein. In embodiments, the phosphoketolase may be xpk1 from Lactobacillus plantarum (ATCC No. BAA-793) (GenBank GI number 28379168). In embodiments, the phosphotransacetylase can be EutD from Lactobacillus plantarum (ATCC No. BAA-793) (GenBank GI number 28377658).

Protein Hydrolysates

Protein hydrolysates (i.e., mixtures of peptides and amino acids) are typically produced from polypeptides during processes of chemical hydrolysis or enzymatic hydrolysis, as described further below. According to the processes of the present invention, protein hydrolysates can be produced via hydrolysis of various process streams (e.g., feedstock slurry 16, wet cake, 24, within the fermentor 30, whole stillage wet cake, thin stillage, syrup).

Chemical hydrolysis: Polypeptides can be completely hydrolyzed by chemical methods, for example, those that are used for amino acid analysis. These include liquid phase and vapor phase acid hydrolysis using 6 N HCl at 110° C. or at higher temperature for shorter times. Polypeptide hydrolysis may also be accelerated by use of microwave heating. Hydrolyses are typically performed as a function of time as serine and threonine are labile and peptide bonds where P1 is isoleucine or valine and P1′ is isoleucine or valine cleave slowly. Following a time course allows one to determine the rate of degradation of serine and threonine and the rate of cleavage of isoleucine and valine. Asparagine and glutamine are hydrolyzed to the respective aspartic and glutamic acids. Cysteine is oxidized to cystine and some oxidation of methionine will occur to the sulfone. Tryptophan is particularly labile to oxidation but can be stabilized to some extent in the presence of thiol reagents (e.g., mercaptoethanesulfonic acid, thioglycolic acid).

Enzymatic Hydrolysis:

Complete conversion of a polypeptide to its component amino acids is often more difficult than acid hydrolysis, owing to the specificity of different proteases. Treatment by broad spectrum proteases (e.g., proteinase K, papain, subtilisin) or consortia of endopeptidases (e.g., pepsin, trypsin, chymotrypsin, and elastase), followed by a combination of exopeptidases (e.g., carboxypeptidases and aminopeptidases) and dipeptidyl and tripeptidyl peptidases are likely to yield a fairly complete hydrolysis, though there may be at the same time some autoproteolysis or cross proteolysis of the added proteases. Pronase, a mixture of proteases secreted by Streptomyces griseus will give a complete or nearly complete hydrolysis of many polypeptides. The choice and concentration of the proteases used may need to be tailored to the polypeptide to be hydrolyzed.

Described in U.S. Pat. No. 5,231,017 is a process for producing ethanol from raw materials that contain fermentable sugars or constituents which can be converted to sugars, comprising the steps of: (a) liquefaction of the raw materials in the presence of an alpha-amylase for obtaining liquefied mash; (b) saccharification of the liquefied mash in the presence of a glucoamylase for obtaining hydrolyzed starch and sugars; (c) fermentation of the hydrolyzed starch and sugars by yeast for obtaining ethanol; (d) recovering alcohol; wherein a protease is introduced in the liquefied mash during the saccharification and/or in the hydrolyze starch and sugars during the fermentation. The yeast advantageously has an increased rate and yield of ethanol production, presumably as a result of increased availability of energy for the yeast's consumption.

According to U.S. Pat. No. 5,231,017, incorporated herein by reference, acid fungal protease may be derived from Aspergillus, Mucor, Rhizopus, Candida, Coriolus, Endothia, Enthomophtora, Irpex, Penicillium, Sclerotium and Torulopsis. In embodiments, the acid fungal protease chosen is thermally stable and is derived from Aspergillus, such as A. niger, A. saitoi, or A. oryzae, from Mucor such as M. pusillus or M. miehei, from Endothia, such as E. parasitica, or from Rhizopus. Most preferably, the acid fungal protease is derived from Aspergillus niger (for example, one acid fungal protease from Aspergillus niger, var. is available under the trade mark AFP-2000 through Solvay Enzymes, Inc.).

The quantity of the acid fungal protease for use in the process herein will depend on the enzymatic activity of the protease, as appreciated by one of skill in the art.

Also available in the art are preparations of glucoamylase and protease blends for simultaneous starch and protein hydrolysis. For example, Fermenzyme® L-400 provides a mixture of ˜10-15% glucoamylase and <1% protease (Genencor®, Palo Alto, Calif.).

Protease use in ethanol production from dry fractionated corn has been studied (Bernardo, Jr., C. Vidal, Ph.D. Thesis, Univ. of Illinois at Urbana-Champaign, 2010). Of particular note, protease NS50045 (Novozymes, Franklinton, N.C.) treatment was reported to result in at least 1% increase in the molar content of all amino acids (except cysteine) in a corn slurry produced from endosperm and germ. For example, a ˜9.3% and ˜7.5% increase in leucine content was measured after protease treatment of the endosperm and germ, respectively.

Methods for Production of Butanol and Fusel Alcohol Mixtures

International Publication No. WO 2011/160030, herein incorporated by reference in its entirety, is directed to a method comprising providing a biomass feedstock slurry comprising fermentable carbon source, undissolved solids, and water; separating at least a portion of the undissolved solids from said slurry whereby (i) an aqueous solution comprising fermentable carbon source and (ii) a wet cake co-product comprising solids are generated; and adding the aqueous solution to a fermentation broth comprising recombinant microorganisms in a fermentation vessel whereby a fermentative product is produced; wherein the biomass processing productivity is improved. In some embodiments of the disclosure therein, the method further comprises a step of liquefying a feedstock to create a biomass feedstock slurry; wherein the feedstock is selected from corn grain, corn cobs, crop residues such as corn husks, corn stover, grasses, corn, wheat, rye, wheat straw, barley, barley straw, hay, rice straw, switchgrass, waste paper, sugar cane bagasse, sorghum, sugar cane, soy, components obtained from milling of grains, cellulosic material, lignocellulosic material, trees, branches, roots, leaves, wood chips, sawdust, shrubs and bushes, vegetables, fruits, flowers, animal manure, and mixtures thereof. The feedstock may be fractionated or unfractionated, wet milled or dry milled. The wet cake may be washed with water to recover oligosaccharides present in the wet cake, said recovered oligosaccharides optionally added to the fermentation vessel. The fermentative product may be a product alcohol selected from the group consisting of methanol, ethanol, propanol, butanol, pentanol, and isomers thereof and the recombinant microorganism may comprise an engineered butanol biosynthetic pathway.

An alcohol production process wherein substrates containing proteins, for example, feedstock solids, can be modified to include a step wherein the biomass feedstock is subjected to chemical or enzymatic hydrolysis to yield protein hydrolysates for use by the recombinant microorganism. An example alcohol production process is depicted in FIG. 12. Biomass feedstock 12 is contacted with liquefaction enzyme 14 in a liquefaction vessel 10 configured to liquefy a feedstock to create a feedstock slurry 16. Feedstock slurry 16 is optionally introduced into a centrifuge to produce wet cake 24 and a carbohydrate-containing stream 22. At least a carbohydrate-containing portion of feedstock slurry 16 is introduced into fermentation vessel where contact occurs with an enzyme or microorganism For example, as indicated in FIG. 12, protein hydrolysates may be generated from substrates present in the fermentation vessel, in the thin stillage, in the whole stillage wet cake, in the syrup, in the backset, or in the wet cake.

One of skill in the art will envision modifying the methods of International Publication No. WO 2011/160030, incorporated herein by reference, to include a step wherein the biomass feedstock is subjected to chemical or enzymatic hydrolysis to yield protein hydrolysates for use by the recombinant microorganism.

For example, in some embodiments, as shown, for example, in FIG. 5A, the system for use in the methods of the invention will include a liquefaction vessel 10 configured to liquefy a feedstock to create a feedstock slurry. In particular, a feedstock 12 can be introduced to an inlet in liquefaction vessel 10. Feedstock 12 can be any suitable biomass material known in the industry including, but not limited to, rye, wheat, cane, or corn that contains a fermentable carbon source such as starch.

The process of liquefying feedstock 12 involves hydrolysis of starch in feedstock 12 into water-soluble sugars and is a conventional process. Any known liquefying processes, as well as the corresponding liquefaction vessel, normally utilized by the industry can be used including, but not limited to, the acid process, the acid-enzyme process, or the enzyme process. Such processes can be used alone or in combination. In some embodiments, the enzyme process can be utilized and an appropriate enzyme 14, for example, alpha-amylase, is introduced to an inlet in liquefaction vessel 10. Water can also be introduced to the liquefaction vessel 10.

The process of liquefying feedstock 12 creates a feedstock slurry 16 that includes sugar (e.g., fermentable carbon) and undissolved solids from the feedstock or biomass. The undissolved solids are non-fermentable portions of feedstock 12. In some embodiments, feedstock 12 can be corn, such as dry milled, unfractionated corn kernels, and the undissolved particles can include germ, fiber, and gluten. Feedstock slurry 16 can be discharged from an outlet of liquefaction vessel 10. In some embodiments, feedstock 12 is corn or corn kernels and feedstock slurry 16 is a corn mash slurry.

A centrifuge 20 configured to remove the undissolved solids from feedstock slurry 16 has an inlet for receiving feedstock slurry 16. Centrifuge 20 agitates or spins feedstock slurry 16 to create a liquid phase or aqueous solution 22 and a solid phase or wet cake 24.

Aqueous solution 22 can include the sugar, for example, in the form of oligosaccharides, and water. Aqueous solution can comprise at least about 10% by weight oligosaccharides, at least about 20% by weight of oligosaccharides, or at least about 30% by weight of oligosaccharides. Aqueous solution 22 can be discharged out an outlet located near the top of centrifuge 20. Aqueous solution can have a viscosity of less than about 20 centipoise. The aqueous solution can comprise less than about 20 g/L of monomeric glucose, more preferably less than about 10 g/L, or less than about 5 g/L of monomeric glucose. Suitable methodology to determine the amount of monomeric glucose is well known in the art. Such suitable methods known in the art include HPLC.

Wet cake 24 can include the undissolved solids, e.g., typically comprising proteins. Wet cake 24 can be discharged from an outlet located near the bottom of centrifuge 20. Wet cake 24 can also include a portion of the sugar and water. Wet cake 24 can be washed with additional water in centrifuge 20 once aqueous solution 22 has been discharged from centrifuge 20. Alternatively, wet cake 24 can be washed with additional water in a separate centrifuge. Washing wet cake 24 will recover the sugar or sugar source (e.g., oligosaccharides) present in the wet cake, and the recovered sugar and water can be recycled to the liquefaction vessel 10.

Wet cake 24 may optionally be treated via chemical hydrolysis or enzymatic hydrolysis to liberate protein hydrolysates present in the wet cake, and the liberated protein hydrolysates, with or without the residual wet cake, can be directly introduced into the fermentor 30 or added to aqueous stream 22.

Centrifuge 20 can be any conventional centrifuge utilized in the industry, including, for example, a decanter bowl centrifuge, three phase decanter centrifuge, disk stack centrifuge, or filtering centrifuge. In some embodiments, removal of the undissolved solids from feedstock slurry 16 can be accomplished by filtration, vacuum filtration, beltfilter, pressure filtration, filtration using a screen, screen separation, grates or grating, porous grating, flotation, hydrocyclone, filter press, screwpress, gravity settler, vortex separator, or any method that may be used to separate solids from liquids. In one embodiment, undissolved solids may be removed from corn mash to form two product streams, for example, an aqueous solution of oligosaccharides which contains a lower concentration of solids as compared to corn mash and a wet cake which contains a higher concentration of solids as compared to corn mash. In addition, a third stream containing corn oil may be generated if a three phase decanter centrifuge is utilized for solids removal from corn mash. As such, a number of product streams may be generated by using different separation techniques or a combination thereof.

A fermentor 30 configured to ferment aqueous solution 22 and protein hydrolysates to produce butanol has an inlet for receiving aqueous solution 22. Fermentor 30 can include a fermentation broth. A yeast is introduced to fermentor 30 to be included in the fermentation broth. In some embodiments, microorganism 32 can be S. cerevisiae. Microorganism 32 consumes the sugar in aqueous solution 22 and the nitrogen in hydrolysates and produces a butanol and fusel alcohol mixture. In some embodiments, microorganism 32 can be a fermentative recombinant microorganism.

The microorganism 32 is engineered to contain a butanol biosynthetic pathway. In some embodiments, the biosynthetic pathway converts pyruvate to a fermentative product. In some embodiments, the biosynthetic pathway comprises at least one heterologous polynucleotide encoding a polypeptide which catalyzes a substrate to product conversion of the biosynthetic pathway. In some embodiments, each substrate to product conversion of the biosynthetic pathway is catalyzed by a polypeptide encoded by a heterologous polynucleotide.

In situ product removal (ISPR) can be utilized to remove the butanol and fusel oil mixture from fermentor 30 as the butanol and fusel oil mixture is produced by the microorganism, for example, by liquid-liquid extraction. Liquid-liquid extraction within the fermentation vessel is described briefly below and can be performed according to the processes described in U.S. Patent Application Publication No. 2009/0305370, the disclosure of which is hereby incorporated in its entirety. In embodiments, liquid-liquid extraction is carried out in the same vessel as the fermentation. In other embodiments, liquid-liquid extraction is performed in a separate vessel downstream of the fermentation. In either case, the extraction may be performed concurrently with the fermentation.

Fermentor 30 has an inlet for receiving an extractant 34. Extractant 34 can be an organic extractant selected from the group consisting of saturated, mono-unsaturated, poly-unsaturated (and mixtures thereof) C₁₂ to C₂₂ fatty alcohols, C₁₂ to C₂₂ fatty acids, esters of C₁₂ to C₂₂ fatty acids, C₁₂ to C₂₂ fatty aldehydes, C₁₂ to C₂₂ fatty amides, and mixtures thereof. The extractant may also be an organic extractant selected from the group consisting of saturated, mono-unsaturated, poly-unsaturated (and mixtures thereof) C₄ to C₂₂ fatty alcohols, C₄ to C₂₈ fatty acids, esters of C₄ to C₂₈ fatty acids, C₄ to C₂₂ fatty aldehydes, and mixtures thereof. Extractant 34 can be an organic extractant such as oleyl alcohol, behenyl alcohol, cetyl alcohol, lauryl alcohol, myristyl alcohol, stearyl alcohol, 1-undecanol, oleic acid, lauric acid, myristic acid, stearic acid, methyl myristate, methyl oleate, undecanal, lauric aldehyde, 20-methylundecanal, and mixtures thereof. Extractant 34 contacts the fermentation broth and the butanol and fusel oil mixture present in the fermentation broth is transferred to extractant 34. A stream 36 of extractant rich with the butanol and fusel oil mixture is discharged through an outlet in fermentor 30. The butanol and fusel oil mixture is subsequently separated from the extractant in stream 36 using conventional techniques. Feed stream may be added to fermentor 30. Fermentor 30 can be any suitable fermentor known in the art.

One of skill in the art will appreciate that the processes described above in conjunction with recombinant microorganisms provided herein can be used to produce renewable hydrocarbon compositions comprising isobutanol and varying amounts of non-isobutanol fusel alcohols. In some embodiments, the processes and microorganisms provided herein are employed to produce a renewable hydrocarbon composition comprising isobutanol and less than about 3% of non-isobutanol fusels by volume. In embodiments, the renewable hydrocarbon composition comprises isobutanol and less than about 2%, less than about 1%, less than about 0.5%, less than about 0.3%, less than about 0.1%, less than about 0.05%, less than about 0.03%, less than about 0.01%, or less than about 0.005% non-isobutanol fusels by volume.

One of skill in the art will also appreciate that it may be desirable to employ the microorganisms and processes provided herein to increase production of non-isobutanol fusels for advantages, but not limited to, those described elsewhere herein for fuel blends. Thus, in embodiments, the renewable hydrocarbon composition comprises isobutanol and greater than about 0.03%, greater than about 0.05%, greater than about 0.07%, greater than about 0.09%, greater than about 1%, greater than about 3%, or greater than about 5% non-isobutanol fusels by volume.

Construction of Recombinant Yeast

Recombinant microorganisms containing the necessary genes that will encode the enzymatic pathway for the conversion of a fermentable carbon substrate to butanol can be constructed using techniques well known in the art (see, for example, U.S. Pat. No. 7,851,188 and US Patent Application Publication No. 2013/0071898A1, both incorporated by reference).

Methods of obtaining desired genes from a genome are common and well known in the art of molecular biology. For example, if the sequence of the gene is known, suitable genomic libraries can be created by restriction endonuclease digestion and can be screened with probes complementary to the desired gene sequence. Once the sequence is isolated, the DNA can be amplified using standard primer-directed amplification methods such as polymerase chain reaction (U.S. Pat. No. 4,683,202) to obtain amounts of DNA suitable for transformation using appropriate vectors. Tools for codon optimization for expression in a heterologous host are readily available. Some tools for codon optimization are available based on the GC content of the host microorganism.

Once the relevant pathway genes are identified and isolated they can be transformed into suitable expression hosts by means well known in the art. Methods for gene expression in recombinant host cells, including, but not limited to, yeast cells are known in the art (see, for example, Methods in Enzymology, Volume 194, Guide to Yeast Genetics and Molecular and Cell Biology (Part A, 2004, Christine Guthrie and Gerald R. Fink (Eds.), Elsevier Academic Press, San Diego, Calif.). The coding region may be from the yeast host cell for transformation and combined with regulatory sequences that are not native to the natural gene. Alternatively, the coding region may be from another host cell; in embodiments, the coding region for an Ehrlich pathway gene and/or butanol pathway gene to be expressed can be codon optimized for the target host cell, as well known to one skilled in the art.

Vectors or cassettes useful for the transformation of a variety of host cells are common and commercially available from companies such as EPICENTRE® (Madison, Wis.), Invitrogen Corp. (Carlsbad, Calif.), Stratagene (La Jolla, Calif.), and New England Biolabs, Inc. (Beverly, Mass.). Typically the vector or cassette contains sequences directing transcription and translation of the relevant gene, a selectable marker, and sequences allowing autonomous replication or chromosomal integration. Suitable vectors comprise a region 5′ of the gene which harbors transcriptional initiation controls and a region 3′ of the DNA fragment which controls transcriptional termination. Both control regions can be derived from genes homologous to the transformed host cell, although it is to be understood that such control regions can also be derived from genes that are not native to the specific species chosen as a production host.

Initiation control regions or promoters, which are useful to drive expression of the relevant pathway coding regions in the desired host cell are numerous and familiar to those skilled in the art. For yeast recombinant host cells, a number of promoters can be used in constructing expression cassettes for genes, including, but not limited to, the following constitutive promoters suitable for use in yeast: FBA1, TDH3 (GPD), ADH1, ILV5, and GPM1; and the following inducible promoters suitable for use in yeast: GAL1, GAL10, OLE1, and CUP1. Other yeast promoters include hybrid promoters UAS(PGK1)-FBA1p, UAS(PGK1)-ENO2p, UAS(FBA1)-PDC1p, UAS(PGK1)-PDC1p and UAS(PGK)-OLE1p (International Publication No. WO 2011/159853, incorporated herein by reference). Suitable transcriptional terminators that can be used in a chimeric gene construct for expression include, but are not limited to, FBA1t, TDH3t, GPM1t, ERG10t, GAL1t, CYC1t, and ADH1t. In embodiments, suitable promoters, transcriptional terminators, and coding regions can be cloned into E. coli-yeast shuttle vectors, and transformed into yeast cells. Such vectors allow strain propagation in both E. coli and yeast strains, and can contain a selectable marker and sequences allowing autonomous replication or chromosomal integration in the desired host. Typically used plasmids in yeast include, but are not limited to, shuttle vectors pRS423, pRS424, pRS425, and pRS426 (American Type Culture Collection, Rockville, Md.), which contain an E. coli replication origin (e.g., pMB1), a yeast 2-micron origin of replication, and a marker for nutritional selection. The selection markers for these four vectors are HIS3 (vector pRS423), TRP1 (vector pRS424), LEU2 (vector pRS425) and URA3 (vector pRS426).

In embodiments, construction of expression vectors with a chimeric gene encoding the described Ehrlich pathway gene(s) and/or butanol pathway gene(s) can be performed by the gap repair recombination method in yeast. In embodiments, a yeast vector DNA is digested (e.g., in its multiple cloning site) to create a “gap” in its sequence. A number of insert DNAs of interest are generated that contain an approximately 21 bp sequence at both the 5′ and the 3′ ends that sequentially overlap with each other, and with the 5′ and 3′ terminus of the vector DNA. For example, to construct a yeast expression vector for “Gene X,” a yeast promoter and a yeast terminator are selected for the expression cassette. The promoter and terminator are amplified from the yeast genomic DNA, and Gene X is either PCR amplified from its source organism or obtained from a cloning vector comprising Gene X sequence. There is at least a 21 bp overlapping sequence between the 5′ end of the linearized vector and the promoter sequence, between the promoter and Gene X, between Gene X and the terminator sequence, and between the terminator and the 3′ end of the linearized vector. The “gapped” vector and the insert DNAs are then co-transformed into a yeast strain and plated on the medium containing the appropriate compound mixtures that allow complementation of the nutritional selection markers on the plasmids. The presence of correct insert combinations can be confirmed by PCR mapping using plasmid DNA prepared from the selected cells. The plasmid DNA isolated from yeast (usually low in concentration) can then be transformed into an E. coli strain, e.g., TOP10, followed by mini preps and restriction mapping to further verify the plasmid construct. Finally the construct can be verified by sequence analysis.

Like the gap repair technique, integration into the yeast genome also takes advantage of the homologous recombination system in yeast. In embodiments, a cassette containing a coding region plus control elements (promoter and terminator) and auxotrophic marker is PCR-amplified with a high-fidelity DNA polymerase using primers that hybridize to the cassette and contain 40-70 base pairs of sequence homology to the regions 5′ and 3′ of the genomic area where insertion is desired. The PCR product is then transformed into yeast and plated on medium containing the appropriate compound mixtures that allow selection for the integrated auxotrophic marker. For example, to integrate “Gene X” into chromosomal location “Y,” the promoter-coding region X-terminator construct is PCR amplified from a plasmid DNA construct and joined to an autotrophic marker (such as URA3) by either SOE PCR or by common restriction digests and cloning. The full cassette, containing the promoter-coding regionX-terminator-URA3 region, is PCR amplified with primer sequences that contain 40-70 bp of homology to the regions 5′ and 3′ of location “Y” on the yeast chromosome. The PCR product is transformed into yeast and selected on growth media lacking uracil. Transformants can be verified either by colony PCR or by direct sequencing of chromosomal DNA. The presence of the introduced enzyme activity in the recombinant host cells disclosed herein can be confirmed using routine methods known in the art. In a non-limiting example, and as described in the Examples herein, transformants can be screened by PCR using primers for the introduced genes. In another non-limiting example, and as described in the Examples herein, transformants can be screened for butanol production.

Promoters, transcriptional terminators, and coding regions can be cloned into a yeast 2 micron plasmid and transformed into yeast cells (Ludwig, et al., Gene 132: 33-40, 1993; U.S. Patent Application Publication No. 2008/0261861A1).

Adjusting the amount of gene expression in a given host may be achieved by varying the level of transcription, such as through selection of native or artificial promoters. In addition, techniques such as the use of promoter libraries to achieve desired levels of gene transcription are well known in the art. Such libraries can be generated using techniques known in the art, for example, by cloning of random cDNA fragments in front of gene cassettes (Goh, et al., AEM 99:17025, 2002), by modulating regulatory sequences present within promoters (Ligr, et al., Genetics 172:2113, 2006), or by mutagenesis of known promoter sequences (Alper, et al., PNAS 102:12678-12683, 2005; Nevoigt, et al., AEM 72:5266, 2006).

Termination control regions can also be derived from various genes native to the hosts. Optionally, a termination site can be unnecessary or can be included.

Certain vectors are capable of replicating in a broad range of host bacteria and can be transferred by conjugation. The complete and annotated sequence of pRK404 and three related vectors-pRK437, pRK442, and pRK442(H) are available. These derivatives have proven to be valuable tools for genetic manipulation in Gram-negative bacteria (Scott, et al., Plasmid 50: 74-79, 2003). Several plasmid derivatives of broad-host-range Inc P4 plasmid RSF1010 are also available with promoters that can function in a range of Gram-negative bacteria. Plasmid pAYC36 and pAYC37, have active promoters along with multiple cloning sites to allow for the heterologous gene expression in Gram-negative bacteria.

Chromosomal gene replacement tools are also widely available. For example, a thermosensitive variant of the broad-host-range replicon pWV101 has been modified to construct a plasmid pVE6002 which can be used to effect gene replacement in a range of Gram-positive bacteria (Maguin, et al., J. Bacteriol. 174: 5633-5638, 1992). Additionally, in vitro transposomes are available to create random mutations in a variety of genomes from commercial sources such as EPICENTRE®.

Fermentation Media

Fermentation media in the present invention must contain suitable carbon substrates. Suitable substrates can include but are not limited to monosaccharides such as glucose and fructose, oligosaccharides such as lactose, maltose, galactose, sucrose, polysaccharides such as starch or cellulose or mixtures thereof and unpurified mixtures from renewable feedstocks such as cheese whey permeate, cornsteep liquor, sugar beet molasses, and barley malt. Additionally the carbon substrate can also be one-carbon substrates such as CO₂, or methanol for which metabolic conversion into key biochemical intermediates has been demonstrated. In addition to one and two carbon substrates methylotrophic microorganisms are also known to utilize a number of other carbon containing compounds such as methylamine, glucosamine and a variety of amino acids for metabolic activity. For example, methylotrophic yeast are known to utilize the carbon from methylamine to form trehalose or glycerol (Bellion et al., Microb. Growth C1 Compd., [Int. Symp.], 7th (1993), 415-32. (eds): Murrell, J. Collin; Kelly, Don P. Publisher: Intercept, Andover, UK). Similarly, various species of Candida will metabolize alanine or oleic acid (Sulter, et al., Arch. Microbiol., 153:485-489, 1990). Hence it is contemplated that the source of carbon utilized in the present invention can encompass a wide variety of carbon containing substrates and will only be limited by the choice of microorganism.

Although it is contemplated that all of the above mentioned carbon substrates and mixtures thereof are suitable in the present invention, in some embodiments, the carbon substrates are glucose, fructose, and sucrose, or mixtures of these with C5 sugars such as xylose and/or arabinose for yeasts cells modified to use C5 sugars. Sucrose can be derived from renewable sugar sources such as sugar cane, sugar beets, cassava, sweet sorghum, and mixtures thereof. Glucose and dextrose can be derived from renewable grain sources through saccharification of starch based feedstocks including grains such as corn, wheat, rye, barley, oats, and mixtures thereof. In addition, fermentable sugars can be derived from renewable cellulosic or lignocellulosic biomass through processes of pretreatment and saccharification, as described, for example, in U.S. Patent Application Publication No. 2007/0031918 A1, which is herein incorporated by reference in its entirety. Biomass refers to any cellulosic or lignocellulosic material and includes materials comprising cellulose, and optionally further comprising hemicellulose, lignin, starch, oligosaccharides and/or monosaccharides. Biomass can also comprise additional components, such as protein and/or lipid. Biomass can be derived from a single source, or biomass can comprise a mixture derived from more than one source; for example, biomass can comprise a mixture of corn cobs and corn stover, or a mixture of grass and leaves. Biomass includes, but is not limited to, bioenergy crops, agricultural residues, municipal solid waste, industrial solid waste, sludge from paper manufacture, yard waste, wood and forestry waste. Examples of biomass include, but are not limited to, corn grain, corn cobs, crop residues such as corn husks, corn stover, grasses, wheat, wheat straw, barley, barley straw, hay, rice straw, switchgrass, waste paper, sugar cane bagasse, sorghum, soy, components obtained from milling of grains, trees, branches, roots, leaves, wood chips, sawdust, shrubs and bushes, vegetables, fruits, flowers, animal manure, and mixtures thereof.

In addition to an appropriate carbon source, fermentation media must contain suitable minerals, salts, cofactors, buffers and other components, known to those skilled in the art, suitable for growth of the cultures and promotion of the enzymatic pathway necessary for butanol production described herein.

Fermentation Conditions

Typically cells are grown at a temperature in the range of about 20° C. to about 40° C. in an appropriate medium. In some embodiments, the cells are grown at a temperature of 20° C., 22° C., 25° C., 27° C., 30° C., 32° C., 35° C., 37° C. or 40° C. Certain cells are more thermo-tolerant and may be grown at higher temperatures such as about 42° C., 45° C., 47° C., and even above 50° C. for short periods of time. Suitable growth media in the present invention are common commercially prepared media such as Luria Bertani (LB) broth, Sabouraud Dextrose (SD) broth or Yeast Medium (YM) broth or broth that includes yeast nitrogen base, ammonium sulfate, and dextrose (as the carbon/energy source) or YPD Medium, a blend of peptone, yeast extract, and dextrose in optimal proportions for growing most Saccharomyces cerevisiae strains. Other defined or synthetic growth media can also be used, and the appropriate medium for growth of the particular microorganism will be known by one skilled in the art of microbiology or fermentation science. The use of agents known to modulate catabolite repression directly or indirectly, e.g., cyclic adenosine 2′,3′-monophosphate (cAMP), can also be incorporated into the fermentation medium.

Suitable pH ranges for the fermentation of yeast are typically from about pH 3.0 to about pH 9.0. In one embodiment, about pH 4.0 to about pH 8.0 is used for the initial condition. In another embodiment, about pH 3.5 to about pH 9.0 is used for the initial condition. In one embodiment, about pH 4.5 to about pH 6.5 is used for the initial condition. In one embodiment, about pH 5.0 to about pH 8.0 is used for the initial condition.

In some embodiments, the contacting of the fermentation medium with the recombinant microorganism is performed under anaerobic or microaerobic conditions.

In some embodiments, the butanol is produced in one or more of the following growth phases: high growth log phase, moderate through static lag phase, stationary phase, steady state growth phase, and combinations thereof.

Industrial Batch and Continuous Fermentations

In some embodiments, the butanol isomers may be produced using batch or continuous fermentation. Butanol may be produced using a batch method of fermentation. A classical batch fermentation is a closed system where the composition of the medium is set at the beginning of the fermentation and not subject to artificial alterations during the fermentation. Thus, at the beginning of the fermentation the medium is inoculated with the desired organism or organisms, and fermentation is permitted to occur without adding anything to the system. Typically, however, a “batch” fermentation is batch with respect to the addition of carbon source and attempts are often made at controlling factors such as pH and oxygen concentration. In batch systems the metabolite and biomass compositions of the system change constantly up to the time the fermentation is stopped. Within batch cultures cells moderate through a static lag phase to a high growth log phase and finally to a stationary phase where growth rate is diminished or halted. If untreated, cells in the stationary phase will eventually die. Cells in log phase generally are responsible for the bulk of production of end product or intermediate.

A variation on the standard batch system is the fed-batch system. Fed-batch fermentation processes are also suitable in the present invention and comprise a typical batch system with the exception that the substrate is added in increments as the fermentation progresses. Fed-batch systems are useful when catabolite repression is apt to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the medium. Measurement of the actual substrate concentration in Fed-Batch systems is difficult and is therefore estimated on the basis of the changes of measurable factors such as pH, dissolved oxygen and the partial pressure of waste gases such as CO₂. Batch and fed-batch fermentations are common and well known in the art and examples may be found in Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, 2^(nd) ed., Sinauer Associates, Inc., Sunderland, Mass. (1989) (“Brock”), or Deshpande, Appl. Biochem. Biotechnol. 36:227, 1992, incorporated herein by reference.

In some embodiments, the butanologen is present at a cell density of at least about 0.5 grams dry cell weight per liter (gdcw/L) prior to contacting with the fermentable carbon substrate. In some embodiments, the butanologen is present at a cell density of at least about 6 gdcw/L to 30 gdcw/L during the first contacting with the carbon substrate. In some embodiments, the cell density of the butanologen may be 6.5 gdcw/L, 7 gdcw/L, 7.5 gdcw/L, 8 gdcw/L, 8.5 gdcw/L, 9 gdcw/L, 9.5 gdcw/L, 10 gdcw/L, 10.5 gdcw/L, 12 gdcw/L, 15 gdcw/L, 17 gdcw/L, 20 gdcw/L, 22 gdcw/L, 25 gdcw/L, 27 gdcw/L or 30 gdcw/L during the first contacting with the carbon substrate.

Butanol isomers, such as isobutanol, may also be produced using continuous fermentation methods. Continuous fermentation is an open system where a defined fermentation medium is added continuously to a bioreactor and an equal amount of conditioned medium is removed simultaneously for processing. Continuous fermentation generally maintains the cultures at a constant high density where cells are primarily in log phase growth. Continuous fermentation allows for the modulation of one factor or any number of factors that affect cell growth or end product concentration. For example, one method will maintain a limiting nutrient such as the carbon source or nitrogen level at a fixed rate and allow all other parameters to moderate. In other systems a number of factors affecting growth can be altered continuously while the cell concentration, measured by medium turbidity, is kept constant. Continuous systems strive to maintain steady state growth conditions and thus the cell loss due to the medium being drawn off must be balanced against the cell growth rate in the fermentation. Methods of modulating nutrients and growth factors for continuous fermentation processes as well as techniques for maximizing the rate of product formation are well known in the art of industrial microbiology and a variety of methods are detailed by Brock.

It is contemplated that the production of butanol, including isobutanol, may be practiced using batch, fed-batch or continuous processes and that any known mode of fermentation would be suitable. Additionally, it is contemplated that cells may be immobilized on a substrate as whole cell catalysts and subjected to fermentation conditions for isobutanol production.

Methods for Butanol/Renewable Hydrocarbon Composition Isolation from the Fermentation Medium

The bioproduced butanol isomers may be recovered from the fermentation medium using methods known in the art. See, e.g., Durre, Appl. Microbiol. Biotechnol. 49:639-648, 1998; Groot, et al., Process. Biochem. 27:61-75, 1992, and references therein. For example, butanol may be isolated from the fermentation medium using methods such as distillation, liquid-liquid extraction, or membrane-based separation. In situ product removal (ISPR) (also referred to as extractive fermentation) can be used to remove butanol (or other fermentative alcohol) from the fermentation vessel as it is produced, thereby allowing the microorganism to produce butanol at high yields. One method for ISPR for removing fermentative alcohol that has been described in the art is flash-fermentation. Another method for ISPR for removing fermentative alcohol that has been described in the art is liquid-liquid extraction. In general, with regard to butanol fermentation, for example, the fermentation medium, which includes the microorganism, is contacted with an organic extractant at a time before the butanol concentration reaches a toxic level. The organic extractant and the fermentation medium form a biphasic mixture. The butanol partitions into the organic extractant phase, decreasing the concentration in the aqueous phase containing the microorganism, thereby limiting the exposure of the microorganism to the inhibitory butanol.

Liquid-liquid extraction can be performed, for example, according to the processes described in U.S. Patent Application Publication No. 2009/0305370, the disclosure of which is hereby incorporated in its entirety. U.S. Patent Application Publication No. 2009/0305370 describes methods for producing and recovering butanol from a fermentation broth using liquid-liquid extraction, the methods comprising the step of contacting the fermentation broth with a water immiscible extractant to form a two-phase mixture comprising an aqueous phase and an organic phase. Typically, the extractant can be an organic extractant selected from the group consisting of saturated, mono-unsaturated, poly-unsaturated (and mixtures thereof) C₁₂ to C₂₂ fatty alcohols, C₁₂ to C₂₂ fatty acids, esters of C₁₂ to C₂₂ fatty acids, C₁₂ to C₂₂ fatty aldehydes, C12 to C22 fatty amides, triglycerides, and mixtures thereof. The extractant(s) for ISPR can be non-alcohol extractants. The ISPR extractant can be an exogenous organic extractant such as oleyl alcohol, behenyl alcohol, cetyl alcohol, lauryl alcohol, myristyl alcohol, stearyl alcohol, 1-undecanol, oleic acid, lauric acid, myristic acid, stearic acid, methyl myristate, methyl oleate, undecanal, lauric aldehyde, 20-methylundecanal, and mixtures thereof.

In some embodiments, an ester can be formed by contacting the alcohol in a fermentation medium with a carboxylic acid (e.g., fatty acids) and a catalyst capable of esterifying the alcohol with the carboxylic acid, as described in International Publication No. WO 2011/159998, which is herein incorporated by reference in its entirety. In such embodiments, the carboxylic acid can serve as an ISPR extractant into which the alcohol esters partition. The carboxylic acid can be supplied to the fermentation vessel and/or derived from the biomass supplying fermentable carbon fed to the fermentation vessel. Lipids present in the feedstock can be catalytically hydrolyzed to carboxylic acid, and the same catalyst (e.g., enzymes) can esterify the carboxylic acid with the alcohol. The catalyst can be supplied to the feedstock prior to fermentation, or can be supplied to the fermentation vessel before or contemporaneously with the supplying of the feedstock. When the catalyst is supplied to the fermentation vessel, alcohol esters can be obtained by hydrolysis of the lipids into carboxylic acid and substantially simultaneous esterification of the carboxylic acid with butanol present in the fermentation vessel. Carboxylic acid and/or native oil not derived from the feedstock can also be fed to the fermentation vessel, with the native oil being hydrolyzed into carboxylic acid. Any carboxylic acid not esterified with the alcohol can serve as part of the ISPR extractant. The extractant containing alcohol esters can be separated from the fermentation medium, and the alcohol can be recovered from the extractant. The extractant can be recycled to the fermentation vessel. Thus, in the case of butanol production, for example, the conversion of the butanol to an ester may reduce the free butanol concentration in the fermentation medium, shielding the microorganism from the toxic effect of increasing butanol concentration. In addition, unfractionated grain can be used as feedstock without separation of lipids therein, since the lipids can be catalytically hydrolyzed to carboxylic acid, thereby decreasing the rate of build-up of lipids in the ISPR extractant.

In situ product removal can be carried out in a batch mode or a continuous mode. In a continuous mode of in situ product removal, product is continually removed from the reactor. In a batchwise mode of in situ product removal, a volume of organic extractant is added to the fermentation vessel and the extractant is not removed during the process. For in situ product removal, the organic extractant can contact the fermentation medium at the start of the fermentation forming a biphasic fermentation medium. Alternatively, the organic extractant can contact the fermentation medium after the microorganism has achieved a desired amount of growth, which can be determined by measuring the optical density of the culture. Further, the organic extractant can contact the fermentation medium at a time at which the product alcohol level in the fermentation medium reaches a preselected level. In the case of butanol production according to some embodiments of the present invention, the carboxylic acid extractant can contact the fermentation medium at a time before the butanol concentration reaches a toxic level, so as to esterify the butanol with the carboxylic acid to produce butanol esters and consequently reduce the concentration of butanol in the fermentation vessel. The ester-containing organic phase can then be removed from the fermentation vessel (and separated from the fermentation broth which constitutes the aqueous phase) after a desired effective titer of the butanol esters is achieved. In some embodiments, the ester-containing organic phase is separated from the aqueous phase after fermentation of the available fermentable sugar in the fermentation vessel is substantially complete.

Because butanol isomers form a low boiling point, azeotropic mixture with water, distillation can only be used to separate the mixture up to its azeotropic composition. Distillation may be used in combination with another separation method to obtain separation around the azeotrope. Methods that may be used in combination with distillation to isolate and purify butanol include, but are not limited to, decantation, liquid-liquid extraction, adsorption, and membrane-based techniques. Additionally, butanol isomers may be isolated using azeotropic distillation using an entrainer (see, for example, Doherty and Malone, Conceptual Design of Distillation Systems, McGraw Hill, New York (2001)).

When distillation is used in combination with decantation to isolate and purify the butanol, the butanol containing fermentation broth is distilled to near the azeotropic composition. Then, the azeotropic mixture is condensed, and the butanol is separated from the fermentation medium by decantation. The decanted aqueous phase may be returned to the first distillation column as reflux. The butanol-rich decanted organic phase may be further purified by distillation in a second distillation column.

When distillation is used in combination with liquid-liquid extraction, the butanol is extracted from the fermentation broth using liquid-liquid extraction with a suitable solvent. The butanol-containing organic phase is then distilled to separate the butanol from the solvent.

When distillation is used in combination with adsorption, the fermentation broth containing the butanol is distilled to near the azeotropic composition and then the remaining water is removed by use of an adsorbent, such as molecular sieves (Aden, et al., Lignocellulosic Biomass to Ethanol Process Design and Economics Utilizing Co-Current Dilute Acid Prehydrolysis and Enzymatic Hydrolysis for Corn Stover, Report NREL/TP-510-32438, National Renewable Energy Laboratory, June 2002).

When distillation is used in combination with pervaporation, the fermentation broth containing the butanol is distilled to near the azeotropic composition, and then the remaining water is removed by pervaporation through a hydrophilic membrane (Guo, et al., J. Membr. Sci. 245:199-210, 2004).

Effective Yield

The presence of butanol and various fusel alcohols can be confirmed using methods known in the art, including, but not limited to those described in U.S. Pat. No. 7,993,889, which is incorporated herein by reference. For example, butanol and fusel alcohol production can be measured by employing chromatographic methods such as high pressure liquid chromatography and/or gas chromatography which are known in the art.

In some embodiments, butanol is produced at an increased effective yield per kg of biomass feedstock. In embodiments, effective yield may be increased by at least about 0.5%, at least about 1%, at least about 2%, or at least about 3%.

In some embodiments, renewable hydrocarbon composition comprising butanol is produced at an increased effective yield per kg of biomass feedstock. In embodiments, effective yield may be increased by at least about 2%, at least about 4%, at least about 5%, at least about 8%, at least about 10%, or at least about 15%.

In some embodiments, fusel alcohol is produced at an increased effective yield per kg of biomass feedstock. In embodiments, effective yield may be increased by at least about 1%, at least about 2%, at least about 4%, at least about 5%, or at least about 8%.

Fuel Blends

Advantages of the disclosed methods may be further recognized in fuel blends comprising the resultant biologically-produced renewable hydrocarbon compositions. In some embodiments provided by the processes herein a mixture of butanol and higher-carbon fusel oils (e.g., isoamyl alcohol and active amyl alcohol) is recovered as the renewable hydrocarbon composition gasoline blending component. In such embodiments, the total carbon-content of recovered renewable hydrocarbon composition gasoline blending component is increased per unit weight of biomass, thus, the compositions can be considered to provide higher energy density when incorporated into gasoline blends; the fusel alcohols isoamyl and active amyl alcohol have about 6.5% greater energy per unit volume of liquid fuel. As a result, the volumetric energy density of the resultant liquid fuel blend is increased per unit weight of biomass processed.

Embodiments provided herein may provide further advantages for economical production of renewable gasoline blends with low vapor pressure, which are desirable for reducing evaporative hydrocarbon emissions. As opposed to the increase in vapor pressure which results from use of ethanol in renewable gasoline blends, butanol provides renewable content while reducing vapor pressure of the blend. Inclusion of the fusel oils isoamyl and active amyl alcohol can enhance this blending benefit because the Reid vapor pressure (RVP) of these fusel oils is about 70% lower than the RVP of butanol. Further, higher alcohols are effective as vapor pressure co-solvents in ethanol-blended fuels, effectively suppressing the large, non-linear vapor pressure increase which occurs at low ethanol concentrations in gasoline; the above renewable compositions incorporating isobutanol and fusel oil (i.e., additional higher alcohols) can be considered equally effective as vapor pressure co-solvents for ethanol-blended fuels.

Fusel oils have also been shown to reduce phase separation of ethanol from gasoline blends when contacted by water, as unavoidably occurs in gasoline distribution systems. Thus, the aforementioned embodiments of butanol with fusel oils may be used in combination of with ethanol to form gasoline blends with high renewable content and improved stability to water contact.

While various embodiments of the present invention have been described above, it should be understood that they have been presented by way of example only, and not limitation. It will be apparent to persons skilled in the relevant art that various changes in form and detail can be made therein without departing from the spirit and scope of the invention. Thus, breadth and scope of the present application should not be limited by any of the above-described exemplary embodiments, but should be defined only in accordance with the claims and their equivalents.

EXAMPLES

The present invention is further defined in the following Examples. It should be understood that these Examples, while indicating embodiments of the invention, are given by way of illustration only. From the above discussion and these Examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various uses and conditions.

General Methods

Materials and methods suitable for the maintenance and growth of bacterial cultures are well known in the art. Techniques suitable for use in the following examples may be found as set out in Manual of Methods for General Bacteriology (Phillipp, et al., eds., American Society for Microbiology, Washington, D C., 1994) or by in Brock, Biotechnology: A Textbook of Industrial Microbiology, Second Edition, Sinauer Associates, Inc., Sunderland, Mass. (1989). All reagents, restriction enzymes and materials used for the growth and maintenance of bacterial cells may be obtained from Sigma-Aldrich Chemicals (St. Louis, Mo.), BD Diagnostic Systems (Sparks, Md.), Invitrogen (Carlsbad, Calif.), HiMedia (Mumbai, India), SD Fine chemicals (India), or Takara Bio Inc. (Shiga, Japan), unless otherwise specified.

Methods for Determining Isobutanol Concentration in Culture Medium

The concentration of isobutanol in the culture medium can be determined by a number of methods known in the art. For example, a specific high performance liquid chromatography (HPLC) method utilized a Shodex SH-1011 column with a Shodex SHG guard column, both purchased from Waters Corporation (Milford, Mass.), with refractive index (RI) detection. Chromatographic separation was achieved using 0.01 M H₂SO₄ as the mobile phase with a flow rate of 0.5 mL/min and a column temperature of 50° C. Isobutanol had a retention time of 46.6 min under the conditions used. Alternatively, gas chromatography (GC) methods are available. For example, a specific GC method utilized an HP-INNOWax column (30 m×0.53 mm id, 1 μm film thickness, Agilent Technologies, Wilmington, Del.), with a flame ionization detector (FID). The carrier gas was helium at a flow rate of 4.5 mL/min, measured at 150° C. with constant head pressure; injector split was 1:25 at 200° C.; oven temperature was 45° C. for 1 min, 45 to 220° C. at 10° C./min, and 220° C. for 5 min; and FID detection was employed at 240° C. with 26 mL/min helium makeup gas. The retention time of isobutanol was 4.5 min.

The meaning of abbreviations is as follows: “sec” means second(s), “min” means minute(s), “h” means hour(s), “nm” means nanometers, “uL” means microliter(s), “mL” means milliliter(s), “mg/mL” means milligram per milliliter, “L” means liter(s), “nm” means nanometers, “mM” means millimolar, “M” means molar, “mmol” means millimole(s), “μmole” means micromole(s), “kg” means kilogram, “g” means gram(s), “μg” means microgram(s) and “ng” means nanogram(s), “PCR” means polymerase chain reaction, “OD” means optical density, “OD600” means the optical density measured at a wavelength of 600 nm, “kDa” means kilodaltons, “g” can also mean the gravitation constant, “bp” means base pair(s), “kbp” means kilobase pair(s), “kb” means kilobase, “%” means percent, “% w/v” means weight/volume percent, “% v/v” means volume/volume percent, “HPLC” means high performance liquid chromatography, “g/L” means gram per liter, “μg/L” means microgram per liter, “ng/μL” means nanogram per microliter, “pmol/μL” means picomol per microliter, “RPM” means rotation per minute, “μmol/min/mg” means micromole per minute per milligram, “w/v” means weight per volume, “v/v” means volume per volume.

Microbial strains may be obtained from The American Type Culture Collection (ATCC), Manassas, Va., unless otherwise noted. All the oligonucleotide primers are synthesized by Sigma-Genosys (Woodlands, Tex.) or Integrated DNA Technologies (IDT) (Coralville, Iowa).

Example 1 Construction of Strain PNY2061

Saccharomyces cerevisiae strain PNY0827 is used as the host cell for further genetic manipulation. PNY0827 refers to a strain derived from S. cerevisiae which has been deposited at the ATCC under the Budapest Treaty on Sep. 22, 2011 at the American Type Culture Collection, Patent Depository 10801 University Boulevard, Manassas, Va. 20110-2209 and has the patent deposit designation PTA-12105.

Deletion of URA3 and Sporulation into Haploids:

In order to delete the endogenous URA3 coding region, a deletion cassette was PCR-amplified from pLA54 (SEQ ID NO:61) which contains a P_(TEF1)-kanMX4-TEF1t cassette flanked by loxP sites to allow homologous recombination in vivo and subsequent removal of the KANMX4 marker. PCR was done by using Phusion® High Fidelity PCR Master Mix (New England BioLabs; Ipswich, Mass.) and primers BK505 (SEQ ID NO:62) and BK506 (SEQ ID NO:63). The URA3 portion of each primer was derived from the 5′ region 180 bp upstream of the URA3 ATG and 3′ region 78 bp downstream of the coding region such that integration of the kanMX4 cassette results in replacement of the URA3 coding region. The PCR product was transformed into PNY0827 using standard genetic techniques (Methods in Yeast Genetics, 2005, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp. 201-202) and transformants were selected on YEP medium supplemented 2% glucose and 100 μg/ml Geneticin® at 30° C. Transformants were screened by colony PCR with primers LA468 (SEQ ID NO:64) and LA492 (SEQ ID NO:65) to verify presence of the integration cassette. A heterozygous diploid was obtained: NYLA98, which has the genotype MATa/α URA3/ura3::loxP-kanMX4-loxP. To obtain haploids, NYLA98 was sporulated using standard methods (Codón, et al., Appl. Environ. Microbiol. 61:630-638, 1995). Tetrads were dissected using a micromanipulator and grown on rich YPE medium supplemented with 2% glucose. Tetrads containing four viable spores were patched onto synthetic complete medium lacking uracil supplemented with 2% glucose, and the mating type was verified by multiplex colony PCR using primers AK109-1 (SEQ ID NO:66), AK109-2 (SEQ ID NO:67), and AK109-3 (SEQ ID NO:68). The resulting identified haploid strains were called NYLA103, which has the genotype: MATα ura3Δ::loxP-kanMX4-loxP, and NYLA106, which has the genotype: MATa ura3Δ::loxP-kanMX4-loxP.

Deletion of His3:

To delete the endogenous HIS3 coding region, a scarless deletion cassette was used. The four fragments for the PCR cassette for the scarless HIS3 deletion were amplified using Phusion® High Fidelity PCR Master Mix (New England BioLabs; Ipswich, Mass.) and CEN.PK 113-7D genomic DNA as template, prepared with a Gentra® Puregene® Yeast/Bact kit (Qiagen; Valencia, Calif.). HIS3 Fragment A was amplified with primer oBP452 (SEQ ID NO:69) and primer oBP453 (SEQ ID NO:70), containing a 5′ tail with homology to the 5′ end of HIS3 Fragment B. HIS3 Fragment B was amplified with primer oBP454 (SEQ ID NO:71), containing a 5′ tail with homology to the 3′ end of HIS3 Fragment A, and primer oBP455 (SEQ ID NO:72) containing a 5′ tail with homology to the 5′ end of HIS3 Fragment U. HIS3 Fragment U was amplified with primer oBP456 (SEQ ID NO:73), containing a 5′ tail with homology to the 3′ end of HIS3 Fragment B, and primer oBP457 (SEQ ID NO:74), containing a 5′ tail with homology to the 5′ end of HIS3 Fragment C. HIS3 Fragment C was amplified with primer oBP458 (SEQ ID NO:75), containing a 5′ tail with homology to the 3′ end of HIS3 Fragment U, and primer oBP459 (SEQ ID NO:76).

PCR products were purified with a PCR Purification kit (Qiagen). HIS3 Fragment AB was created by overlapping PCR by mixing HIS3 Fragment A and HIS3 Fragment B and amplifying with primers oBP452 (SEQ ID NO:69) and oBP455 (SEQ ID NO:72). HIS3 Fragment UC was created by overlapping PCR by mixing HIS3 Fragment U and HIS3 Fragment C and amplifying with primers oBP456 (SEQ ID NO:73) and oBP459 (SEQ ID NO:76). The resulting PCR products were purified on an agarose gel followed by a Gel Extraction kit (Qiagen). The HIS3 ABUC cassette was created by overlapping PCR by mixing HIS3 Fragment AB and HIS3 Fragment UC and amplifying with primers oBP452 (SEQ ID NO:69) and oBP459 (SEQ ID NO:76). The PCR product was purified with a PCR Purification kit (Qiagen).

Competent cells of NYLA106 were transformed with the HIS3 ABUC PCR cassette and were plated on synthetic complete medium lacking uracil supplemented with 2% glucose at 30° C. Transformants were screened to verify correct integration by replica plating onto synthetic complete medium lacking histidine and supplemented with 2% glucose at 30° C. Genomic DNA preps were made to verify the integration by PCR using primers oBP460 (SEQ ID NO:77) and LA135 (SEQ ID NO:78) for the 5′ end and primers oBP461 (SEQ ID NO:79) and LA92 (SEQ ID NO:80) for the 3′ end. The URA3 marker was recycled by plating on synthetic complete medium supplemented with 2% glucose and 5-FOA at 30° C. following standard protocols. Marker removal was confirmed by patching colonies from the 5-FOA plates onto SD-URA medium to verify the absence of growth. The resulting identified strain, called PNY2003 has the genotype: MATa ura3Δ::loxP-kanMX4-loxP his3Δ.

Deletion of PDC1:

To delete the endogenous PDC1 coding region, a deletion cassette was PCR-amplified from pLA59 (SEQ ID NO:81), which contains a URA3 marker flanked by degenerate loxP sites to allow homologous recombination in vivo and subsequent removal of the URA3 marker. PCR was done by using Phusion® High Fidelity PCR Master Mix (New England BioLabs; Ipswich, Mass.) and primers LA678 (SEQ ID NO:82) and LA679 (SEQ ID NO:83). The PDC1 portion of each primer was derived from the 5′ region 50 bp downstream of the PDC1 start codon and 3′ region 50 bp upstream of the stop codon such that integration of the URA3 cassette results in replacement of the PDC1 coding region but leaves the first 50 bp and the last 50 bp of the coding region. The PCR product was transformed into PNY2003 using standard genetic techniques and transformants were selected on synthetic complete medium lacking uracil and supplemented with 2% glucose at 30° C. Transformants were screened to verify correct integration by colony PCR using primers LA337 (SEQ ID NO:84), external to the 5′ coding region and LA135 (SEQ ID NO:78), an internal primer to URA3. Positive transformants were then screened by colony PCR using primers LA692 (SEQ ID NO:85) and LA693 (SEQ ID NO:86), internal to the PDC1 coding region. The URA3 marker was recycled by transforming with pLA34 (SEQ ID NO:87) containing the CRE recombinase under the GAL1 promoter and plated on synthetic complete medium lacking histidine and supplemented with 2% glucose at 30° C. Transformants were plated on rich medium supplemented with 0.5% galactose to induce the recombinase. Marker removal was confirmed by patching colonies to synthetic complete medium lacking uracil and supplemented with 2% glucose to verify absence of growth. The resulting identified strain, called PNY2008 has the genotype: MATa ura3Δ::loxP-kanMX4-loxP his3Δ, pdc1Δ::loxP71/66.

Deletion of PDC5:

To delete the endogenous PDC5 coding region, a deletion cassette was PCR-amplified from pLA59 (SEQ ID NO:81), which contains a URA3 marker flanked by degenerate loxP sites to allow homologous recombination in vivo and subsequent removal of the URA3 marker. PCR was done by using Phusion® High Fidelity PCR Master Mix (New England BioLabs; Ipswich, Mass.) and primers LA722 (SEQ ID NO:88) and LA733 (SEQ ID NO:89). The PDC5 portion of each primer was derived from the 5′ region 50 bp upstream of the PDC5 start codon and 3′ region 50 bp downstream of the stop codon such that integration of the URA3 cassette results in replacement of the entire PDC5 coding region. The PCR product was transformed into PNY2008 using standard genetic techniques and transformants were selected on synthetic complete medium lacking uracil and supplemented with 1% ethanol at 30° C. Transformants were screened to verify correct integration by colony PCR using primers LA453 (SEQ ID NO:90), external to the 5′ coding region and LA135 (SEQ ID NO:78), an internal primer to URA3. Positive transformants were then screened by colony PCR using primers LA694 (SEQ ID NO:91) and LA695 (SEQ ID NO:92), internal to the PDC5 coding region. The URA3 marker was recycled by transforming with pLA34 (SEQ ID NO:87) containing the CRE recombinase under the GAL1 promoter and plated on synthetic complete medium lacking histidine and supplemented with 1% ethanol at 30° C. Transformants were plated on rich YEP medium supplemented with 1% ethanol and 0.5% galactose to induce the recombinase. Marker removal was confirmed by patching colonies to synthetic complete medium lacking uracil and supplemented with 1% ethanol to verify absence of growth. The resulting identified strain, called PNY2009 has the genotype: MATa ura3Δ::loxP-kanMX4-loxP his3Δ, pdc1Δ::loxP71/66 pdc5Δ::loxP71/66.

Deletion of FRA2:

The FRA2 deletion was designed to delete 250 bp from the 3′ end of the coding sequence, leaving the first 113 bp of the FRA2 coding sequence intact. An in-frame stop codon was present 7 bp downstream of the deletion. The four fragments for the PCR cassette for the scarless FRA2 deletion were amplified using Phusion® High Fidelity PCR Master Mix (New England BioLabs; Ipswich, Mass.) and CEN.PK 113-7D genomic DNA as template, prepared with a Gentra® Puregene® Yeast/Bact kit (Qiagen; Valencia, Calif.). FRA2 Fragment A was amplified with primer oBP594 (SEQ ID NO:93) and primer oBP595 (SEQ ID NO:94), containing a 5′ tail with homology to the 5′ end of FRA2 Fragment B. FRA2 Fragment B was amplified with primer oBP596 (SEQ ID NO:95), containing a 5′ tail with homology to the 3′ end of FRA2 Fragment A, and primer oBP597 (SEQ ID NO:96), containing a 5′ tail with homology to the 5′ end of FRA2 Fragment U. FRA2 Fragment U was amplified with primer oBP598 (SEQ ID NO:97), containing a 5′ tail with homology to the 3′ end of FRA2 Fragment B, and primer oBP599 (SEQ ID NO:98), containing a 5′ tail with homology to the 5′ end of FRA2 Fragment C. FRA2 Fragment C was amplified with primer oBP600 (SEQ ID NO:99), containing a 5′ tail with homology to the 3′ end of FRA2 Fragment U, and primer oBP601 (SEQ ID NO:100).

PCR products were purified with a PCR Purification kit (Qiagen). FRA2 Fragment AB was created by overlapping PCR by mixing FRA2 Fragment A and FRA2 Fragment B and amplifying with primers oBP594 (SEQ ID NO:93) and oBP597 (SEQ ID NO:96). FRA2 Fragment UC was created by overlapping PCR by mixing FRA2 Fragment U and FRA2 Fragment C and amplifying with primers oBP598 (SEQ ID NO:97) and oBP601 (SEQ ID NO:100). The resulting PCR products were purified on an agarose gel followed by a Gel Extraction kit (Qiagen). The FRA2 ABUC cassette was created by overlapping PCR by mixing FRA2 Fragment AB and FRA2 Fragment UC and amplifying with primers oBP594 (SEQ ID NO:93) and oBP601 (SEQ ID NO:100). The PCR product was purified with a PCR Purification kit (Qiagen).

To delete the endogenous FRA2 coding region, the scarless deletion cassette obtained above was transformed into PNY2009 using standard techniques and plated on synthetic complete medium lacking uracil and supplemented with 1% ethanol. Genomic DNA preps were made to verify the integration by PCR using primers oBP602 (SEQ ID NO:101) and LA135 (SEQ ID NO:78) for the 5′ end, and primers oBP602 (SEQ ID NO:101) and oBP603 (SEQ ID NO:102) to amplify the whole locus. The URA3 marker was recycled by plating on synthetic complete medium supplemented with 1% ethanol and 5-FOA (5-Fluoroorotic Acid) at 30° C. following standard protocols. Marker removal was confirmed by patching colonies from the 5-FOA plates onto synthetic complete medium lacking uracil and supplemented with 1 ethanol to verify the absence of growth. The resulting identified strain, PNY2037, has the genotype: MATa ura3Δ::loxP-kanMX4-loxP his3Δ, pdc1Δ::loxP71/66 pdc5Δ::loxP71/66 fra2Δ.

Addition of 2 Micron Plasmid Fragments:

The loxP71-URA3-loxP66 marker was PCR-amplified using Phusion® DNA polymerase (New England BioLabs; Ipswich, Mass.) from pLA59 (SEQ ID NO:81), and transformed along with the LA811 and LA817 (SEQ ID NOs:103 and 104) and LA812 and LA818 (SEQ ID NOs:105 and 106) 2-micron plasmid fragments into strain PNY2037 on SE-URA plates at 30° C. The resulting strain PNY2037 2μ::loxP71-URA3-loxP66 was transformed with pLA34 (pRS423::cre) (SEQ ID NO:87) and selected on SE-HIS-URA plates at 30° C. Transformants were patched onto YP-1% galactose plates and allowed to grow for 48 hrs at 30° C. to induce Cre recombinase expression. Individual colonies were then patched onto SE-URA, SE-HIS, and YPE plates to confirm URA3 marker removal. The resulting identified strain, PNY2050, has the genotype: MATa ura30::loxP-kanMX4-loxP, his3Δ, pdc1Δ::loxP71/66 pdc1Δ::loxP71/66 fra2Δ, 2-micron.

Deletion of GPD2:

To delete the endogenous GPD2 coding region, a deletion cassette was PCR-amplified from pLA59 (SEQ ID NO:81), which contains a URA3 marker flanked by degenerate loxP sites to allow homologous recombination in vivo and subsequent removal of the URA3 marker. PCR was done by using Phusion® High Fidelity PCR Master Mix (New England BioLabs; Ipswich, Mass.) and primers LA512 (SEQ ID NO:107) and LA513 (SEQ ID NO:108). The GPD2 portion of each primer was derived from the 5′ region 50 bp upstream of the GPD2 start codon and 3′ region 50 bp downstream of the stop codon such that integration of the URA3 cassette results in replacement of the entire GPD2 coding region. The PCR product was transformed into PNY2050 using standard genetic techniques and transformants were selected on synthetic complete medium lacking uracil and supplemented with 1% ethanol at 30° C. Transformants were screened to verify correct integration by colony PCR using primers LA516 (SEQ ID NO:109), external to the 5′ coding region and LA135 (SEQ ID NO:78), internal to URA3. Positive transformants were then screened by colony PCR using primers LA514 (SEQ ID NO:110) and LA515 (SEQ ID NO:111), internal to the GPD2 coding region. The URA3 marker was recycled by transforming with pLA34 (SEQ ID NO:87) containing the CRE recombinase under the GAL1 promoter and plated on synthetic complete medium lacking histidine and supplemented with 1% ethanol at 30° C. Transformants were plated on rich medium supplemented with 1% ethanol and 0.5% galactose to induce the recombinase. Marker removal was confirmed by patching colonies to synthetic complete medium lacking uracil and supplemented with 1% ethanol to verify absence of growth. The resulting identified strain, PNY2056, has the genotype: MATa ura3Δ::loxP-kanMX4-loxP his3Δ, pdc1Δ::loxP71/66 pdc5Δ::loxP71/66 fra2Δ, 2-micron gpd2Δ.

Deletion of YMR226 and Integration of AlsS:

To delete the endogenous YMR226C coding region, an integration cassette was PCR-amplified from pLA71 (SEQ ID NO:112), which contains a gene encoding B. subtilis acetolactate synthase (amino acid SEQ ID NO:135) with a FBA1 promoter and a CYC1 terminator (i.e., P_(FBA1)-alsS_Bs-CYC1t), and a URA3 marker flanked by degenerate loxP sites to allow homologous recombination in vivo and subsequent removal of the URA3 marker. PCR was done by using KAPA HiFi from Kapa Biosystems, Woburn, Mass. and primers LA829 (SEQ ID NO:113) and LA834 (SEQ ID NO:114). The YMR226C portion of each primer was derived from the first 60 bp of the coding sequence and 65 bp that are 409 bp upstream of the stop codon. The PCR product was transformed into PNY2056 using standard genetic techniques and transformants were selected on synthetic complete medium lacking uracil and supplemented with 1% ethanol at 30° C. Transformants were screened to verify correct integration by colony PCR using primers N1257 (SEQ ID NO:115), external to the 5′ coding region and LA740, internal to the FBA1 promoter. Positive transformants were then screened by colony PCR using primers N1257 (SEQ ID NO:115) and LA830 (SEQ ID NO:116), internal to the YMR226C coding region, and primers LA830 (SEQ ID NO:116), external to the 3′ coding region, and LA92 (SEQ ID NO:80), internal to the URA3 marker. The URA3 marker was recycled by transforming with pLA34 (SEQ ID NO:87) containing the CRE recombinase under the GAL1 promoter and plated on synthetic complete medium lacking histidine and supplemented with 1% ethanol at 30° C. Transformants were plated on rich medium supplemented with 1% ethanol and 0.5% galactose to induce the recombinase. Marker removal was confirmed by patching colonies to synthetic complete medium lacking uracil and supplemented with 1% ethanol to verify absence of growth. The resulting identified strain, PNY2061, has the genotype: MATa ura3Δ::loxP-kanMX4-loxP his3Δ, pdc1Δ::loxP71/66 pdc5Δ::loxP71/66 fra2Δ, 2-micron gpd2Δ ymr226cΔ::P_(FBA1)-alsS_Bs-CYC1t-loxP71/66.

Example 2 (Prophetic) Construction of Strain with Up-Regulated Valine Transaminase Activity

This example describes the construction of a PNY2061-derived strain that has increased expression of the BAT1 and/or BAT2 branched chain transaminases.

In order to integrate a chimeric BAT1 gene (i.e., in addition to the native BAT1 gene) for increased expression, an integration cassette is PCR-amplified from pLA59::FBA1p-BAT1-CYC1t (SEQ ID NO:117), which contains the S. cerevisiae BAT1 gene with a FBA1 promoter and a CYC1 terminator, and a URA3 marker flanked by degenerate loxP sites to allow homologous recombination in vivo and subsequent removal of the URA3 marker. PCR is done by using KAPA HiFi from Kapa Biosystems, Woburn, Mass. with primers designed to add 75 bp of sequence upstream and downstream of the PDC6 locus to allow homologous recombination and replacement of the PDC6 coding region. The PCR product is transformed into PNY2061 using standard genetic techniques and transformants is selected on synthetic complete medium lacking uracil and supplemented with 1% ethanol at 30° C. Transformants are screened to verify correct integration by colony PCR using primers internal to the BAT1 gene and external to the PDC6 locus. The URA3 marker is recycled by transforming with pLA34 (SEQ ID NO:87) containing the CRE recombinase under the GAL1 promoter and plating on synthetic complete medium lacking histidine and supplemented with 1% ethanol at 30° C. Transformants are plated on rich medium supplemented with 1% ethanol and 0.5% galactose to induce the recombinase. Marker removal is confirmed by patching colonies to synthetic complete medium lacking uracil and supplemented with 1% ethanol to verify absence of growth. The resulting identified strain, T0001, has the genotype: MATa ura3Δ::loxP-kanMX4-loxP his3Δ, pdc1Δ::loxP71/66 pdc5Δ::loxP71/66 fra2Δ, 2-micron gpd2Δ ymr226cΔ::P_(FBA1)-alsS_Bs-CYC1t-loxP71/66 pdc6Δ:: P_(FBA1)-BAT1-CYC1t-loxP71/66.

In order to integrate a chimeric BAT2 gene (i.e., in addition to the native BAT2 gene) for increased expression, an integration cassette is PCR-amplified from pLA59::FBA1p-BAT2-CYC1t (SEQ ID NO:118), which contains the S. cerevisiae BAT2 gene with a FBA1 promoter and a CYC1 terminator, and a URA3 marker flanked by degenerate loxP sites to allow homologous recombination in vivo and subsequent removal of the URA3 marker. PCR is done by using KAPA HiFi (Kapa Biosystems) with primers designed to add 75 bp of sequence upstream and downstream of the ADH1 locus to allow homologous recombination and replacement of the ADH1 coding region. The PCR product is transformed into PNY2061 using standard genetic techniques and transformants is selected on synthetic complete medium lacking uracil and supplemented with 1% ethanol at 30° C. Transformants are screened to verify correct integration by colony PCR using primers internal to the BAT2 gene and external to the ADH1 locus. The URA3 marker is recycled by transforming with pLA34 (SEQ ID NO:87) containing the CRE recombinase under the GAL1 promoter and plating on synthetic complete medium lacking histidine and supplemented with 1% ethanol at 30° C. Transformants are plated on rich medium supplemented with 1% ethanol and 0.5% galactose to induce the recombinase. Marker removal is confirmed by patching colonies to synthetic complete medium lacking uracil and supplemented with 1% ethanol to verify absence of growth. The resulting identified strain, T0002, has the genotype: MATa ura3Δ::loxP-kanMX4-loxP his3Δ, pdc1Δ::loxP71/66 pdc5Δ::loxP71/66 fra2Δ, 2-micron gpd2Δ ymr226cΔ::P_(FBA1)-alsS_Bs-CYC1t-loxP71/66 adh1Δ:: P_(FBA1)-BAT2-CYC1t-loxP71/66.

Since BAT1 and BAT2 are capable of catalyzing conversion of the branched chain amino acids to their α-keto acid counterparts (i.e., L-isoleucine→2-keto-3-methyl-valerate, L-leucine→α-ketoisocaproate and L-valine→2-keto-isovalerate, respectively), it is expected that upregulation of either of these transaminases will lead to increased flux through the Ehrlich pathway resulting in an increased concentration of fusel oil from these amino acids. Thus, for example, if the PNY2061-derived strain having increased expression of BAT1 and/or BAT2 is grown in a fermentation medium comprising a suitable concentration of protein hydrolysates, an increased concentration of active amyl alcohol and methylvalerate may be produced from L-isoleucine and/or an increased concentration of isoamyl alcohol and isovalerate may be produced from Leucine and/or an increased concentration of isobutanol and isobutyrate may be produced from L-valine (wherein the first product is the fusel alcohol and the second product listed is the fusel acid, respectively).

Example 3 (Prophetic) Construction of Strain with Up-Regulated Leucine/Isoleucine Transaminase Activity

This example describes the construction of a PNY2061-derived strain that has increased expression of the ARO8 and/or ARO9 branched chain transaminases, with optional up-regulation of the ARO10 decarboxylase.

In order to integrate a chimeric ARO8 gene (i.e., in addition to the native ARO8 gene) for increased expression, an integration cassette is PCR-amplified from pLA59::TDH3p-ARO8-ADH1t (SEQ ID NO:119), which contains the S. cerevisiae ARO8 gene with a TDH3 promoter and a ADH1 terminator, and a URA3 marker flanked by degenerate loxP sites to allow homologous recombination in vivo and subsequent removal of the URA3 marker. PCR is done by using KAPA HiFi from Kapa Biosystems, Woburn, Mass. with primers designed to add 75 bp of sequence upstream and downstream of the MET15 locus to allow homologous recombination and replacement of the MET15 coding region. The PCR product is transformed into PNY2061 using standard genetic techniques and transformants is selected on synthetic complete medium lacking uracil and supplemented with 1% ethanol at 30° C. Transformants are screened to verify correct integration by colony PCR using primers internal to the ARO8 gene and external to the MET15 locus. The URA3 marker is recycled by transforming with pLA34 (SEQ ID NO:87) containing the CRE recombinase under the GAL1 promoter and plating on synthetic complete medium lacking histidine and supplemented with 1% ethanol at 30° C. Transformants are plated on rich medium supplemented with 1% ethanol and 0.5% galactose to induce the recombinase. Marker removal are confirmed by patching colonies to synthetic complete medium lacking uracil and supplemented with 1% ethanol to verify absence of growth. The resulting identified strain, T0003, has the genotype: MATa ura3Δ::loxP-kanMX4-loxP his3Δ, pdc1Δ::loxP71/66 pdc5Δ::loxP71/66 fra2Δ, 2-micron gpd2Δ ymr226cΔ::P_(FBA1)-alsS_Bs-CYC1t-loxP71/66 met15Δ:: P_(TDH3)-ARO8-ADH1t-loxP71/66.

In order to integrate a chimeric ARO9 gene (i.e., in addition to the native ARO9 gene) for increased expression, an integration cassette is PCR-amplified from pLA59::TDH3p-ARO9-ADHt1 (SEQ ID NO:120), which contains the S. cerevisiae ARO9 gene with a TDH3 promoter and a ADH1 terminator, and a URA3 marker flanked by degenerate loxP sites to allow homologous recombination in vivo and subsequent removal of the URA3 marker. PCR is done by using KAPA HiFi from Kapa Biosystems, Woburn, Mass. with primers designed to add 75 bp of sequence upstream and downstream of the BDH1 locus to allow homologous recombination and replacement of the BDH1 coding region. The PCR product is transformed into PNY2061 using standard genetic techniques and transformants is selected on synthetic complete medium lacking uracil and supplemented with 1% ethanol at 30° C. Transformants are screened to verify correct integration by colony PCR using primers internal to the ARO9 gene and external to the BDH1 locus. The URA3 marker is recycled by transforming with pLA34 (SEQ ID NO:87) containing the CRE recombinase under the GAL1 promoter and plating on synthetic complete medium lacking histidine and supplemented with 1% ethanol at 30° C. Transformants are plated on rich medium supplemented with 1% ethanol and 0.5% galactose to induce the recombinase. Marker removal are confirmed by patching colonies to synthetic complete medium lacking uracil and supplemented with 1% ethanol to verify absence of growth. The resulting identified strain, T0004, has the genotype: MATa ura3Δ::loxP-kanMX4-loxP his3Δ, pdc1Δ::loxP71/66 pdc5Δ::loxP71/66 fra2Δ, 2-micron gpd2Δ ymr226cΔ::P_(FBA1)-alsS_Bs-CYC1t-loxP71/66 bdh1Δ:: P_(TDH3)-ARO9-ADH1t-loxP71/66.

Optionally, in order to integrate a chimeric ARO10 gene (i.e., in addition to the native ARO10 gene) for increased expression, an integration cassette is PCR-amplified from pLA59::TDH3p-ARO10-ADH1t (SEQ ID NO:121), which contains the S. cerevisiae ARO10 gene with a TDH3 promoter and a ADH1 terminator, and a URA3 marker flanked by degenerate loxP sites to allow homologous recombination in vivo and subsequent removal of the URA3 marker. PCR is done by using KAPA HiFi from Kapa Biosystems, Woburn, Mass. with primers designed to add 75 bp of sequence upstream and downstream of the GPD2 locus to allow homologous recombination and replacement of the GPD2 coding region. The PCR product is transformed into PNY2061 using standard genetic techniques and transformants is selected on synthetic complete medium lacking uracil and supplemented with 1% ethanol at 30° C. Transformants are screened to verify correct integration by colony PCR using primers internal to the ARO10 gene and external to the GPD2 locus. The URA3 marker is recycled by transforming with pLA34 (SEQ ID NO:87) containing the CRE recombinase under the GAL1 promoter and plating on synthetic complete medium lacking histidine and supplemented with 1% ethanol at 30° C. Transformants are plated on rich medium supplemented with 1% ethanol and 0.5% galactose to induce the recombinase. Marker removal are confirmed by patching colonies to synthetic complete medium lacking uracil and supplemented with 1% ethanol to verify absence of growth. The resulting identified strain, T0005, has the genotype: MATa ura3Δ::loxP-kanMX4-loxP his3Δ, pdc1Δ::loxP71/66 pdc5Δ::loxP71/66 fra2Δ, 2-micron gpd2Δ ymr226cΔ::P_(FBA1)-alsS_Bs-CYC1t-loxP71/66 bdh1Δ:: P_(TDH3)-ARO9-ADH1t-loxP71/66 gpd2Δ:: P_(TDH3)-ARO10-ADH1t-loxP71/66.

Since ARO8 and ARO9 are capable of catalyzing conversion of the aromatic amino acids to their α-keto acid counterparts (i.e., L-tyrosine p-hydroxyphenylpyruvate, L-phenylalanine phenylpyruvate, L-tryptophan indolepyruvate, respectively), it is expected that upregulation of either of these aromatic aminotransferase will lead to increased flux through the Ehrlich pathway resulting in an increased concentration of fusel oil from these amino acids. Thus, for example, if the PNY2061-derived strain having increased expression of ARO8 and/or ARO9 is grown in a fermentation medium comprising a suitable concentration of protein hydrolysates, an increased concentration of p-hydroxyphenylethanol and p-hydroxyphenylacetate may be produced from L-tyrosine and/or an increased concentration of 2-phenylethanol and 2-phenylacetate may be produced from L-phenylalanine and/or an increased concentration of tryptophol and 2-(indol-3-yl)ethanoate may be produced from L-tryptophan.

Similarly, ARO10 catalyzes conversion of α-keto acids to fusel aldehydes (e.g., 2-keto-3-methyl-valerate 2-methylbutanal, α-ketoisocaproate 3-methylbutanal, phenylpyruvate phenylacetaldehyde, indolepyruvate indole acetaldehyde, respectively), it is expected that upregulation of this decarboxylase will lead to increased flux through the Ehrlich pathway resulting in an increased concentration of fusel oil from these α-keto acids.

Example 4 (Prophetic) Construction of Strain with Up-Regulated Valine and Leucine/Isoleucine Transaminase Activity

This example describes the construction of a PNY2061-derived strain that has increased expression of a combination of BAT1, BAT2, ARO8, and ARO9 branched chain transaminases, with optional up-regulation of the ARO10 decarboxylase. Using the molecular biology methods outlined in Example 2 and Example 3, the transformation constructs can be sequentially integrated into the genome of PNY2061 (Example 1) with step-wise recycling of the URA3 marker. For example, the genotype of a strain, T0006, with all integrations described in Examples 2-3, would be: MATa ura3Δ::loxP-kanMX4-loxP his3Δ, pdc1Δ::loxP71/66 pdc5Δ::loxP71/66 fra2Δ, 2-micron gpd2Δ ymr226cΔ::P_(FBA1)-alsS_Bs-CYC1t-loxP71/66 pdc64:: P_(FBA1)-BAT1-CYC1t-loxP71/66 adh1Δ:: P_(FBA1)-BAT2-CYC1t-loxP71/66 met15Δ:: P_(TDH3)-ARO8-ADH1t-loxP71/66 bdh1Δ:: P_(TDH3)-ARO9-ADH1t-loxP71/66 gpd2Δ:: P_(TDH3)-ARO10-ADH1t-loxP71/66.

Example 5 (Prophetic) Fermentation with Strains Producing Isobutanol and Increased Transaminase Activity

This example describes fermentation with a PNY2061-derived strain that produces isobutanol and that has increased expression of a combination of BAT1, BAT2, ARO8, and ARO9 branched chain transaminases, with optional up-regulation of the ARO10 decarboxylase. A protease, such as Fermenzyme® L-400, is used to liberate increased amounts of free amino acids from the corn mash fermentation media.

The host strain PNY2061 (Example 1) or PNY2061-derived strain with increased transaminase activity T0006 (Example 4) is transformed with plasmids pHR81-ILV5p-K9SB2 (SEQ ID NO:122) and pLA84 (SEQ ID NO:123), creating the isobutanologens T0007, and T0008, respectively. Plasmids are introduced by lithium acetate transformation method (Methods in Yeast Genetics, 2005, page 113), and transformants are selected on synthetic complete medium, minus histidine and uracil, with 1% ethanol as carbon source. Transformants are then transferred to plates containing synthetic complete medium, minus histidine and uracil, with 2% glucose as carbon source and either ethanol (0.05%) or acetate (2 mM) as a C2 supplement. Freezer vials are made by dilution of log-phase cultures with 45% glycerol to a final glycerol concentration of 15% (w/v).

Plasmid pHR81-ILV5p-K9SB2 (SEQ ID NO:122) contains the Anaerostipes caccae K9SB2 KARI gene (SEQ ID NO:124) driven by ILV5 promoter and ILV5 terminator in pHR81 plasmid backbone. Plasmid pLA84 (SEQ ID NO:123) contains the pRS423 plasmid backbone and: (i) the Streptococcus mutans ilvD gene (SEQ ID NO:126) driven by the FBA1 promoter and FBA1 terminator; (ii) the Beijerinckia indica ADH gene (SEQ ID NO:129) driven by the GPM1 promoter and the ADH1 terminator; and, (iii) the Listeria grayi KivD gene (SEQ ID NO:128) driven by the TDH3 promoter and the TDH3 terminator.

Corn mash centrate is produced by removing undissolved solids from the com mash prior to fermentation. Four extractive fermentations are conducted side-by side, two with liquefied com mash as the sugar source (solids not removed) and two with liquefied mash centrate (aqueous solution of oligosaccharides) obtained by removing most of the undissolved solids from liquefied com mash. Oleyl alcohol (OA) is added to extract the product (i-BuOH) from the broth as it is formed.

Approximately 31 kg of liquefied com mash is prepared in a 30 L jacketed glass resin kettle. The reactor is outfitted with mechanical agitation, temperature control, and pH control. The protocol used is as follows: mix ground com with tap water (40 wt % com on a dry basis), heat the slurry to 55° C. while agitating at 250 rpm, adjust pH to 5.8 with either NaOH or H₂SO₄, add a dilute aqueous solution of alpha-amylase (0.16 wt % on a dry com basis), hold at 55° C. for 60 min, heat to 95° C., adjust pH to 5.8, hold at 95° C. for 120 min while maintaining pH at 5.8 to complete liquefaction. The mash is transferred into sterile centrifuge bottles to prevent contamination.

The com used is whole kernel yellow corn from Pioneer Hi-Bred International, Inc. (Johnston, Iowa). It is ground in a pilot-scale hammer-mill using a 1 mm screen. The moisture content of the ground com is measured to be about 12 wt %, and the starch content of the ground com is measured to be about 71.4 wt % on a dry com basis. The alpha-amylase enzyme used is Spezyme® Fred-L (Genencor®, Palo Alto, Calif.). The amounts of the ingredients used are: 14.1 kg of ground com (12% moisture), 16.9 kg of tap water, a solution of alpha-amylase consisting of 19.5 g of Spezyme® Fred-L in 2.0 kg of water. The alpha-amylase is sterile filtered. A total of 0.21 kg of NaOH (17 wt %) is added throughout the run to control pH. It is estimated that the liquefied com mash contained approximately 28 wt % (about 280 g/L) of liquefied starch based on the com loading used, starch content of the com, and assuming all the starch is hydrolyzed during liquefaction. The mash is prepared with a higher concentration of oligosaccharides than is desired in the fermentations to allow for dilution when adding the nutrients, inoculum, glucoamylase, and base to the initial fermentation broth. After dilution by addition of nutrients, inoculum, glucoamylase, and base, the expected total initial soluble sugars in the mash (solids not removed) is about 250 g/L.

About 13.9 kg of the liquefied mash is centrifuged using a bottle centrifuge which contained six 1 L bottles. The centrifuge is operated at 5000 rpm (7260 RCF) for 20 min at room temperature. The mash is separated into about 5.5 kg of clarified centrate and about 8.4 kg of wet cake (the pellet at the bottom of the centrifuge bottles). The split, defined as (amount of centrate)/(amount of mash fed), is about (5.5 kg/13.9 kg)=40%. Solids are not removed from the mash charged to the 2010Y034 and 2010Y036 fermentations described below. The centrate charged to fermentations 2010Y033 and 2010Y035 (also described below) is produced by removing (by centrifugation) most of the suspended solids from mash according to the protocols above.

The S. cerevisiae strains T0007 and T0008 are grown to 0.55-1.1 g/L dcw (OD₆₀₀ I.3-2.6—Thermo Helios a Thermo Fisher Scientific Inc., Waltham, Mass.) in seed flasks from a frozen culture. The culture is grown at 26° C. in an incubator rotating at 300 rpm. The frozen culture is previously stored at −80° C. The composition of the first seed flask medium is: 3.0 g/L dextrose; 3.0 g/L ethanol, anhydrous; 3.7 g/L ForMedium™ Synthetic Complete Amino Acid (Kaiser) Drop-Out: without HIS, without URA (Reference No. DSCKI62CK); and, 6.7 g/L Difco Yeast Nitrogen Base without amino acids (No. 291920).

Twelve milliliters from the first seed flask culture is transferred to a 2 L flask and grown at 30° C. in an incubator rotating at 300 rpm. The second seed flask has 220 mL of the following medium: 30.0 g/L dextrose; 5.0 g/L ethanol, anhydrous; 3.7 g/L ForMedium™ Synthetic Complete Amino Acid (Kaiser) Drop-Out: without HIS, without URA (Reference No. DSCKI62CK); 6.7 g/L Difco Yeast Nitrogen Base without amino acids (No. 291920); and, 0.2 M MES Buffer titrated to pH 5.5-6.0.

The culture is grown to 0.55-1.1 g/L dcw (OD₆₀₀ I.3-2.6). An addition of 30 mL of a solution containing 200 g/L peptone and 100 g/L yeast extract is added at this cell concentration. Then an addition of 300 mL of 0.2 μM filter sterilized Cognis, 90-95% oleyl alcohol is added to the flask. The culture continues to grow to >4 g/L dcw (OD₆₀₀>10) before being harvested and added to the fermentation.

A glass jacked, 2 L fermentor (Sartorius AG, Goettingen, Germany) is charged with liquefied mash either with or without solids (centrate). A pH probe (Hamilton Easyferm Plus K8, part number: 238627, Hamilton Bonaduz AG, Bonaduz, Switzerland) is calibrated through the Sartorius DCU-3 Control Tower Calibration menu. The zero is calibrated at pH=7. The span is calibrated at pH=4. The probe is then placed into the fermentor, through the stainless steel head plate. A dissolved oxygen probe (P02 probe) is also placed into the fermentor through the head plate. Tubing used for delivering nutrients, seed culture, extracting solvent, and base are attached to the head plate and the ends were foiled. The entire fermentor is placed into a Steris (Steris Corporation, Mentor, Ohio) autoclave and sterilized in a liquid cycle for 30 min. The fermentor is removed from the autoclave and placed on a load cell. The jacket water supply and return line was connected to the house water and clean drain, respectively. The condenser cooling water in and water out lines are connected to a 6-L recirculating temperature bath running at 7° C. The vent line that transfers the gas from the fermentor is connected to a transfer line that is connected to a Thermo mass spectrometer (Prima dB, Thermo Fisher Scientific Inc., Waltham, Mass.). The sparger line is connected to the gas supply line. The tubing for adding nutrients, extract solvent, seed culture, and base is plumbed through pumps or clamped closed. The autoclaved material, 0.9% w/v NaCl is drained prior to the addition of liquefied mash.

7.0 ml/L (post-inoculation volume) of ethanol (200 proof, anhydrous) is added just prior to inoculation. Thiamine (final concentration 20 mg/L) is added just prior to inoculation. Nicotinic acid (100 mg/L) is added just prior to inoculation. The fermentor's p0₂ probe is calibrated to zero while N₂ is being added to the fermentor. The fermentor's p0₂ probe is calibrated to its span with sterile air sparging at 300 rpm. The fermentor is inoculated after the second seed flask was >4 g/L dcw. The shake flask is removed from the incubator/shaker for 5 min allowing a phase separation of the oleyl alcohol phase and the aqueous phase. The 55 mL of the aqueous phase is transferred to a sterile, inoculation bottle. The inoculum is pumped into the fermentor through a peristaltic pump. One liter (post-inoculation volume) of oleyl alcohol is added immediately after inoculation.

The fermentor is operated at 30° C. for the entire growth and production stages. The pH is allowed to drop from a pH between 5.7-5.9 to a control set-point of 5.2 without adding any acid. The pH is controlled for the remainder of the growth and production stage at a pH=5.2 with ammonium hydroxide. Sterile air is added to the fermentor, through the sparger, at 0.3 slpm for the remainder of the growth and production stages. The p02 is set to be controlled at 3.0% by the Sartorius DCU-3 Control Box PID control loop, using stir control only, with the stirrer minimum being set to 300 rpm and the maximum being set to 2000 rpm. The glucose is supplied through simultaneous saccharification and fermentation of the liquefied com mash by adding either Distillase® L-400 (glucoamylase) or Fermenzyme® L-400 (glucoamylase plus protease; Genencor®, Palo Alto, Calif.). The glucose is kept excess (1-50 g/L) for as long as starch was available for saccharification.

Process air is analyzed on a Thermo Prima (Thermo Fisher Scientific Inc., Waltham, Mass.) mass spectrometer. This is the same process air that was sterilized and then added to each fermentor. Each fermentor's off-gas is analyzed on the same mass spectrometer. The gases calibrated are: nitrogen, oxygen, isobutanol, argon, and CO₂. Based on the analysis of the off-gas of each fermentor, the amount of isobutanol stripped, oxygen consumed, and CO₂ respired into the off-gas is measured by using the mass spectrometer's mole fraction analysis and gas flow rates (mass flow controller) into the fermentor. The gassing rate per hour is calculated and used to integrate that rate over the course of the fermentation.

Aqueous samples are refrigerated until ready for processing. Samples are removed from refrigeration for one hr to bring to room temperature. Approximately 300 μL of sample is transferred with a m1000 Variable Channel BioHit pipette with 100-1000 μL BioHit pipette tips into a 0.2 μm centrifuge filter (Nanosep MF modified nylon centrifuge filter), then centrifuged using a Eppendorf 5415C for five min at 14,000 rpm. Approximately 200 uL of filtered sample is transferred into a 1.8 ml auto sampler vial with a 2504 glass vial insert with polymer feet. A screw cap with PTFE septa, is used to cap the vial before vortexing the sample with a Vortex-Genie® set at 2700 rpm. Samples are then run on Agilent 1200 series LC equipped with binary, isocratic pumps, vacuum degasser, heated column compartment, sampler cooling system, UV DAD detector and RI detector. The column used is an Aminex HPX-87H, 300×7.8 with a Bio-Rad Cation H refill, 30×4.6 guard column. Column temperature is 40° C., with a mobile phase of 0.01 N sulfuric acid, at a flow rate of 0.6 mL/min for 40 min.

Samples from the oleyl alcohol phase are refrigerated until ready for processing. Samples are removed from the refrigerator for one hr to bring to room temperature. Approximately 1504 of sample is transferred using a m1000 Variable Channel BioHit pipette with 100-1000 μL BioHit pipette tips into a 1.8 ml auto sampler vial with a 250 μL glass vial insert with polymer feet. A screw cap with PTFE septa is used to cap the vial. Samples are then run on Agilent 7890A GC with a 7683B injector and a G2614A auto sampler. The column is a HP-InnoWax column (30 m×0.32 mm ID, 0.25 μm film). The carrier gas is helium at a flow rate of 1.5 mL/min measured at 45° C. with constant head pressure; injector split was 1:50 at 225° C.; oven temperature was 45° C. for 1.5 min, 45° C. to 160° C. at 10° C./min for 0 min, then 230° C. at 35° C./min for 14 min for a run time of 29 min. Flame ionization detection is used at 260° C. with 40 mL/min helium makeup gas.

Increased product yields of fusel alcohols (isobutanol, isoamyl alcohol, and active amyl alcohol) are detected in fermentations using the T0008 strain with increased transaminase activity. Protease addition further increases the product yield of fusel alcohols in T0008 strains with increased transaminase activity.

Relative product yields (expected) Active amyl Isobutanol Isoamyl alcohol alcohol without protease addition Strain T0007 ++ ++ ++ Strain T0008 +++ +++ +++ with protease addition Strain T0007 +++ +++ +++ Strain T0008 ++++ ++++ ++++ 

1-18. (canceled)
 19. A method for producing a butanol and fusel oil mixture from a biomass feedstock comprising: a) providing a biomass feedstock; b) processing the biomass feedstock to produce a processed feedstock slurry comprising protein hydrolysates and oligosaccharides; c) saccharifying the oligosaccharides of the processed feedstock slurry to produce a fermentation composition comprising fermentable sugars and protein hydrolysates; d) fermenting a recombinant yeast in the presence of the fermentation composition, said recombinant yeast comprising: (i) a heterologous butanol biosynthetic pathway for production of butanol; and, (ii) at least one upregulated Ehrlich pathway gene for production of fusel oil; whereby a butanol and fusel oil mixture is produced; and, e) recovering the butanol and fusel oil mixture; wherein the yield of the butanol and fusel oil mixture per kilogram of biomass feedstock is increased as compared to that produced by a recombinant yeast which does not comprise at least one upregulated Ehrlich pathway gene and recovered.
 20. The method of claim 19, step (b) wherein processing the biomass feedstock to produce a processed feedstock slurry comprising protein hydrolysates and oligosaccharides comprises liquefying the biomass feedstock in the presence of at least one protease.
 21. The method of claim 19, step (b) wherein processing the biomass feedstock to produce a processed feedstock slurry comprising protein hydrolysates and oligosaccharides comprises: 1) liquefying the biomass feedstock to create a feedstock slurry comprising oligosaccharides, undissolved solids, and water; 2) separating at least a portion of the undissolved solids from the feedstock slurry of step (1) to generate: i. an aqueous solution comprising oligosaccharides; and ii. a wet cake co-product comprising solids; 3) hydrolyzing the wet cake co-product of step (2)(ii) to produce protein hydrolysates; and, 4) mixing the aqueous solution comprising oligosaccharides of step (2)(i) with the protein hydrolysates of step (3) to produce a processed feedstock slurry comprising protein hydrolysates and oligosaccharides.
 22. The method of claim 21, step (2), wherein the undissolved solids are separated from the feedstock slurry by a means selected from the group consisting of: decanter bowl centrifugation, tricanter centrifugation, disk stack centrifugation, filtering centrifugation, decanter centrifugation, filtration, vacuum filtration, beltfilter, pressure filtration, screen filtration, screen separation, grating, porous grating, flotation, hydroclone, filter press, screwpress, gravity settler, vortex separator, or combinations thereof.
 23. The method of claim 21, wherein the wet cake co-product is hydrolyzed by a means selected from the group consisting of: acid hydrolysis, base hydrolysis and enzymatic hydrolysis.
 24. The method of claim 21, wherein the feedstock in the fermentation process comprises one or more fermentable sugars derived from corn grain, corn cobs, crop residues such as corn husks, corn stover, grasses, wheat, rye, wheat straw, barley, barley straw, hay, rice straw, switchgrass, waste paper, sugar cane bagasse, sorghum, sugar cane, soy, components obtained from milling of grains, cellulosic material, lignocellulosic material, trees, branches, roots, leaves, wood chips, sawdust, shrubs and bushes, vegetables, fruits, flowers, animal manure, and mixtures thereof.
 25. The method of claim 19, wherein the recombinant yeast is Saccharomyces, Schizosaccharomyces, Hansenula, Candida, Kluyveromyces, Yarrowia, Issatchenkia, or Pichia.
 26. (canceled)
 27. The method of claim 21, wherein the at least one upregulated Ehrlich pathway gene is selected from the group consisting of: a. a gene encoding a polypeptide having aromatic aminotransferase activity, said polypeptide having at least about 90% identity to ARO8 (SEQ ID NO:2) or ARO9 (SEQ ID NO:4); b. a gene encoding a polypeptide having branched chain amino acid transferase activity, said polypeptide having at least about 90% identity to BAT1 (SEQ ID NO:8) or BAT2 (SEQ ID NO:10); c. a gene encoding a polypeptide having Phenylpyruvate decarboxylase activity, said polypeptide having at least about 90% identity to ARO10 (SEQ ID NO:6); d. a gene encoding a polypeptide having Pyruvate decarboxylase activity, said polypeptide having at least about 90% identity to PDC1 (SEQ ID NO:12), PDC5 (SEQ ID NO:14) or PDC6 (SEQ ID NO:16); e. a gene encoding a polypeptide having Alpha-ketoisocaproate decarboxylase activity, said polypeptide having at least about 90% identity to THI3 (SEQ ID NO:18); f. a gene encoding a polypeptide having Alcohol dehydrogenase activity, said polypeptide having at least about 90% identity to ADH1 (SEQ ID NO:20), ADH2 (SEQ ID NO:22), ADH3 (SEQ ID NO:24), ADH4 (SEQ ID NO:26), ADH5 (SEQ ID NO:28), ADH6 (SEQ ID NO:30) or SFA1 (SEQ ID NO:32); g. a gene encoding a polypeptide having aryl-alcohol dehydrogenase activity, said polypeptide having at least about 90% identity to AAD3 (SEQ ID NO:34), AAD4 (SEQ ID NO:36), AAD6 (SEQ ID NO:30), AAD10 (SEQ ID NO:40), AAD14 (SEQ ID NO:42), AAD15 (SEQ ID NO:44), AAD16 (SEQ ID NO:46) or YPL088W (SEQ ID NO:48); h. a gene encoding a polypeptide having Aldehyde dehydrogenase activity, said polypeptide having at least about 90% identity to ALD2 (SEQ ID NO:52), ALD3 (SEQ ID NO:54), ALD4 (SEQ ID NO:56), ALD5 (SEQ ID NO:58) or ALD6 (SEQ ID NO:60); and i. a gene encoding a polypeptide having ATP-binding ATP transporter activity, said polypeptide having at least about 90% identity to PDR12 (SEQ ID NO:50).
 28. The method of claim 21, wherein the butanol biosynthetic pathway is selected from the group consisting of: a) an isobutanol biosynthetic pathway comprising the following substrate to product conversions: pyruvate to acetolactate, acetolactate to 2,3-dihydroxyisovalerate, 2,3-dihydroxyisovalerate to α-ketoisovalerate, α-ketoisovalerate to isobutyraldehyde, and isobutyraldehyde to isobutanol; b) an isobutanol biosynthetic pathway comprising the following substrate to product conversions: pyruvate to acetolactate, acetolactate to 2,3-dihydroxyisovalerate, 2,3-dihydroxyisovalerate to α-ketoisovalerate, α-ketoisovalerate to isobutyryl-CoA, isobutyryl-CoA to isobutyraldehyde, and isobutyraldehyde to isobutanol; c) an isobutanol biosynthetic pathway comprising the following substrate to product conversions: pyruvate to acetolactate, acetolactate to 2,3-dihydroxyisovalerate, 2,3-dihydroxyisovalerate to α-ketoisovalerate, α-ketoisovalerate to valine, valine to isobutylamine, isobutylamine to isobutyraldehyde, and isobutyraldehyde to isobutanol; d) a 1-butanol biosynthetic pathway comprising the following substrate to product conversions: acetyl-CoA to acetoacetyl-CoA, acetoacetyl-CoA to 3-hydroxybutyryl-CoA, 3-hydroxybutyryl-CoA to crotonyl-CoA, crotonyl-CoA to butyryl-CoA, butyryl-CoA to butyraldehyde, and butyraldehyde to 1-butanol; e) a 2-butanol biosynthetic pathway comprising the following substrate to product conversions: pyruvate to alpha-acetolactate, alpha-acetolactate to acetoin, acetoin to 2,3-butanediol, 2,3-butanediol to 2-butanone, and 2-butanone to 2-butanol. 29-32. (canceled)
 33. A method for producing a renewable hydrocarbon composition comprising isobutanol, the method comprising: a) providing a feedstock slurry comprising protein hydrolysates and fermentable carbohydrate; b) adding the feedstock slurry to a fermentation medium; c) contacting the fermentation medium comprising the feedstock slurry with a recombinant yeast host cell capable of producing a renewable hydrocarbon composition from both protein hydrolysates and fermentable carbohydrate; and d) recovering a renewable hydrocarbon composition from the fermentation medium by distillation; wherein the recombinant yeast host cell comprises: i) an isobutanol production pathway comprising enzymes which catalyze the following substrate to product conversions: pyruvate to acetolactate, acetolactate to 2,3-dihydroxyisovalerate, 2,3-dihydroxyisovalerate to α-ketoisovalerate, α-ketoisovalerate to isobutyraldehyde, and isobutyraldehyde to isobutanol; ii) at least one heterologous enzyme which catalyzes a substrate to product conversion of i); and iii) at least one genetic modification which increases the activity of LEU4, at least one genetic modification which increases the activity of LEU9, at least one genetic modification which increases the activity of ILV1, or a combination of such genetic modifications.
 34. The method of claim 33, wherein the at least one heterologous enzyme which catalyzes a substrate to product conversion is acetolactate synthase, ketol-acid reductoisomerase, dihydroxyacid dehydratase, ketoisovalerate decarboxylase, or alcohol dehydrogenase.
 35. The method of claim 33, wherein at least two heterologous enzymes catalyze substrate to product conversions of i).
 36. The method of claim 33, wherein at least three heterologous enzymes catalyze substrate to product conversions of i).
 37. The method of claim 33, wherein the genetic modification which increases the activity of LEU4, LEU9, or ILV1 comprises an upregulation of LEU4, LEU9, or ILV1 genes.
 38. The method of claim 33, wherein the recombinant yeast host cell comprises a disruption of an endogenous polynucleotide encoding a polypeptide having pyruvate decarboxylase activity or an endogenous polypeptide having pyruvate decarboxylase activity.
 39. The method of claim 38, wherein the recombinant yeast host cell comprises a modification to reduce glycerol-3-phosphate dehydrogenase activity.
 40. The method of claim 33, wherein the recombinant yeast host cell comprises modifications in polynucleotides encoding URA3 (orotidine-5′-phosphate decarboxylase), HIS3 (imidazoleglycerol-phosphate dehydratase), FRA2 (iron repressor protein), CCC1 (putative vacuolar Fe2+/Mn2+ transporter), GPD2 (glycerol-2-phosphate dehydrogenase) or acetolactate reductase or polypeptides having URA3, HIS3, FRA2, CCC1, GPD2, or acetolactate reductase activity, or combinations thereof.
 41. The method of claim 33, wherein the recombinant yeast host cell is Saccharomyces, Schizosaccharomyces, Hansenula, Candida, Kluyveromyces, Yarrowia, Issatchenkia, or Pichia.
 42. The method of claim 33, wherein the renewable hydrocarbon composition comprises isobutanol.
 43. The method of claim 33, further comprising blending an amount of the renewable hydrocarbon composition with gasoline whereby a fuel blend is produced. 